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Maize Breeding for Low Nitrogen Inputs in Agriculture: Mechanisms Underlying the Tolerance to the Abiotic Stress. STRESSES 2023. [DOI: 10.3390/stresses3010011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Nitrogen (N) is essential for sustaining life on Earth and plays a vital role in plant growth and thus agricultural production. The excessive use of N fertilizers not only harms the economy, but also the environment. In the context of the environmental impacts caused by agriculture, global maize improvement programs aim to develop cultivars with high N-use efficiency (NUE) to reduce the use of N fertilizers. Since N is highly mobile in plants, NUE is related to numerous little-known morphophysiological and molecular mechanisms. In this review paper we present an overview of the morpho-physiological adaptations of shoot and root, molecular mechanisms involved in plant response to low nitrogen environment, and the genetic effects involved in the control of key traits for NUE. Some studies show that the efficiency of cultivars growing under low N is related to deep root architecture, more lateral roots (LR), and sparser branching of LR, resulting in lower metabolic costs. The NUE cultivars also exhibit more efficient photosynthesis, which affects plant growth under suboptimal nitrogen conditions. In this sense, obtaining superior genotypes for NUE can be achieved with the exploitation of heterosis, as non-additive effects are more important in the expression of traits associated with NUE.
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2
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Limami AM, Cukier C, Hirel B. 15N-labelling of Leaves Combined with GC-MS Analysis as a Tool for Monitoring the Dynamics of Nitrogen Incorporation into Amino Acids. Methods Mol Biol 2023; 2642:151-161. [PMID: 36944877 DOI: 10.1007/978-1-0716-3044-0_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
Labeling plant material such as detached leaves with 15NH4+ is a very instrumental method for the characterization of metabolic pathways of mineral nitrogen assimilation and incorporation into amino acids. A procedure of labeling, followed by amino acid extraction, purification, and derivatization for gas chromatography coupled to mass spectrometry (GC/MS) analysis, is presented. The rationale of heavy isotope abundance calculations and amino acid quantification is detailed. This method is adaptable to various plant species and various kinds of investigations, such as elucidating physiological changes occurring as a result of gene mutations (overexpression or inhibition) in natural variants or genetically modified crops, or characterization of metabolic fluxes in genotypes exhibiting contrasted physiological or developmental adaptive responses to biotic and/or abiotic environmental stresses. Furthermore, the benefit of working on detached organs or pieces of organs is to investigate finely the metabolism of species that are not amenable to laboratory work, such as plants growing in natural environments or under agricultural conditions in the field.
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Affiliation(s)
- Anis M Limami
- Univ Angers, INRAE, IRHS, SFR QUASAV, Angers, France.
| | | | - Bertrand Hirel
- INRAE, Institut Jean-Pierre Bourgin, Agro-ParisTech, Université Paris-Saclay, Paris, France
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3
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Band Phosphorus and Sulfur Fertilization as Drivers of Efficient Management of Nitrogen of Maize (Zea mays L.). PLANTS 2022; 11:plants11131660. [PMID: 35807612 PMCID: PMC9268923 DOI: 10.3390/plants11131660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/15/2022] [Accepted: 06/20/2022] [Indexed: 11/17/2022]
Abstract
Increasing the efficiency of nitrogen use (NUE) from mineral fertilizers is one of the most important priorities of modern agriculture. The objectives of the present study were to assess the role of different nitrogen (N), phosphorus (P) and sulfur (S) rates on maize grain yield (GY), crop residue biomass, NUE indices, N concentration in plants during the growing season, N management indices and to select the most suitable set of NUE indicators. The following factors were tested: band application of di-ammonium phosphate and ammonium sulphate mixture (NPS fertilizer at rates 0, 8.7, 17.4, 26.2 kg ha−1 of P) and different total N rates (0, 60, 120, 180 kg ha−1 of N). In each year of the study, a clear trend of increased GY after NP(S) band application was observed. A particularly positive influence of that factor was confirmed at the lowest level of N fertilization. On average, the highest GY values were obtained for N2P3 and N3P1 treatments. The total N uptake and NUE indices also increased after the band application. In addition, a trend of improved N remobilization efficiency and the N contribution of remobilized N to grain as a result of band application of NP(S) was observed. Among various NUE indices, internal N utilization efficiency (IE) exhibited the strongest, yet negative, correlation with GY, whereas IE was a function of the N harvest index.
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4
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Kumar P, Eriksen RL, Simko I, Shi A, Mou B. Insights into nitrogen metabolism in the wild and cultivated lettuce as revealed by transcriptome and weighted gene co-expression network analysis. Sci Rep 2022; 12:9852. [PMID: 35701518 PMCID: PMC9197935 DOI: 10.1038/s41598-022-13954-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 05/31/2022] [Indexed: 11/08/2022] Open
Abstract
Large amounts of nitrogen fertilizers applied during lettuce (Lactuca sativa L.) production are lost due to leaching or volatilization, causing severe environmental pollution and increased costs of production. Developing lettuce varieties with high nitrogen use efficiency (NUE) is the eco-friendly solution to reduce nitrogen pollution. Hence, in-depth knowledge of nitrogen metabolism and assimilation genes and their regulation is critical for developing high NUE varieties. In this study, we performed comparative transcriptomic analysis of the cultivated lettuce (L. sativa L.) and its wild progenitor (L. serriola) under high and low nitrogen conditions. A total of 2,704 differentially expressed genes were identified. Key enriched biological processes included photosynthesis, oxidation-reduction process, chlorophyll biosynthetic process, and cell redox homeostasis. The transcription factors (TFs) belonging to the ethylene responsive factor family and basic helix-loop-helix family were among the top differentially expressed TFs. Using weighted gene co-expression network analysis we constructed nine co-expression modules. Among these, two modules were further investigated because of their significant association with total nitrogen content and photosynthetic efficiency of photosystem II. Three highly correlated clusters were identified which included hub genes for nitrogen metabolism, secondary metabolites, and carbon assimilation, and were regulated by cluster specific TFs. We found that the expression of nitrogen transportation and assimilation genes varied significantly between the two lettuce species thereby providing the opportunity of introgressing wild alleles into the cultivated germplasm for developing lettuce cultivars with more efficient use of nitrogen.
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Affiliation(s)
- Pawan Kumar
- Crop Improvement and Protection Research Unit, USDA-ARS, 1636 E Alisal St, Salinas, CA, 93905, USA.
| | - Renee L Eriksen
- Forage Seed and Cereal Research Unit, USDA-ARS, 3450 SW Campus Way, Corvallis, OR, 97331, USA
| | - Ivan Simko
- Crop Improvement and Protection Research Unit, USDA-ARS, 1636 E Alisal St, Salinas, CA, 93905, USA
| | - Ainong Shi
- Department of Horticulture, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Beiquan Mou
- Crop Improvement and Protection Research Unit, USDA-ARS, 1636 E Alisal St, Salinas, CA, 93905, USA
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5
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Javed T, I I, Singhal RK, Shabbir R, Shah AN, Kumar P, Jinger D, Dharmappa PM, Shad MA, Saha D, Anuragi H, Adamski R, Siuta D. Recent Advances in Agronomic and Physio-Molecular Approaches for Improving Nitrogen Use Efficiency in Crop Plants. FRONTIERS IN PLANT SCIENCE 2022; 13:877544. [PMID: 35574130 PMCID: PMC9106419 DOI: 10.3389/fpls.2022.877544] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 03/11/2022] [Indexed: 05/05/2023]
Abstract
The efficiency with which plants use nutrients to create biomass and/or grain is determined by the interaction of environmental and plant intrinsic factors. The major macronutrients, especially nitrogen (N), limit plant growth and development (1.5-2% of dry biomass) and have a direct impact on global food supply, fertilizer demand, and concern with environmental health. In the present time, the global consumption of N fertilizer is nearly 120 MT (million tons), and the N efficiency ranges from 25 to 50% of applied N. The dynamic range of ideal internal N concentrations is extremely large, necessitating stringent management to ensure that its requirements are met across various categories of developmental and environmental situations. Furthermore, approximately 60 percent of arable land is mineral deficient and/or mineral toxic around the world. The use of chemical fertilizers adds to the cost of production for the farmers and also increases environmental pollution. Therefore, the present study focused on the advancement in fertilizer approaches, comprising the use of biochar, zeolite, and customized nano and bio-fertilizers which had shown to be effective in improving nitrogen use efficiency (NUE) with lower soil degradation. Consequently, adopting precision farming, crop modeling, and the use of remote sensing technologies such as chlorophyll meters, leaf color charts, etc. assist in reducing the application of N fertilizer. This study also discussed the role of crucial plant attributes such as root structure architecture in improving the uptake and transport of N efficiency. The crosstalk of N with other soil nutrients plays a crucial role in nutrient homeostasis, which is also discussed thoroughly in this analysis. At the end, this review highlights the more efficient and accurate molecular strategies and techniques such as N transporters, transgenes, and omics, which are opening up intriguing possibilities for the detailed investigation of the molecular components that contribute to nitrogen utilization efficiency, thus expanding our knowledge of plant nutrition for future global food security.
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Affiliation(s)
- Talha Javed
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- Department of Agronomy, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Indu I
- Indian Council of Agricultural Research (ICAR)-Indian Grassland and Fodder Research Institute, Jhansi, India
| | - Rajesh Kumar Singhal
- Indian Council of Agricultural Research (ICAR)-Indian Grassland and Fodder Research Institute, Jhansi, India
| | - Rubab Shabbir
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- Department of Plant Breeding and Genetics, Seed Science and Technology, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Adnan Noor Shah
- Department of Agricultural Engineering, Khwaja Fareed University of Engineering and Information Technology, Rahim Yar Khan, Pakistan
| | - Pawan Kumar
- Indian Council of Agricultural Research (ICAR)-Central Institute for Arid Horticulture, Bikaner, India
| | - Dinesh Jinger
- Research Centre, Indian Council of Agricultural Research (ICAR)-Indian Institute of Soil and Water Conservation, Anand, India
| | - Prathibha M. Dharmappa
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Horticultural Research, Bengaluru, India
| | - Munsif Ali Shad
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene, Hubei Hongshan Laboratory, Wuhan, China
| | - Debanjana Saha
- Centurion University of Technology and Management, Jatni, India
| | - Hirdayesh Anuragi
- Indian Council of Agricultural Research (ICAR)- Central Agroforestry Research Institute, Jhansi, India
| | - Robert Adamski
- Faculty of Process and Environmental Engineering, Łódź University of Technology, Łódź, Poland
| | - Dorota Siuta
- Faculty of Process and Environmental Engineering, Łódź University of Technology, Łódź, Poland
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6
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Chand Jha U, Nayyar H, Mantri N, Siddique KHM. Non-Coding RNAs in Legumes: Their Emerging Roles in Regulating Biotic/Abiotic Stress Responses and Plant Growth and Development. Cells 2021; 10:cells10071674. [PMID: 34359842 PMCID: PMC8306516 DOI: 10.3390/cells10071674] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/24/2021] [Accepted: 06/28/2021] [Indexed: 12/28/2022] Open
Abstract
Noncoding RNAs, including microRNAs (miRNAs), small interference RNAs (siRNAs), circular RNA (circRNA), and long noncoding RNAs (lncRNAs), control gene expression at the transcription, post-transcription, and translation levels. Apart from protein-coding genes, accumulating evidence supports ncRNAs playing a critical role in shaping plant growth and development and biotic and abiotic stress responses in various species, including legume crops. Noncoding RNAs (ncRNAs) interact with DNA, RNA, and proteins, modulating their target genes. However, the regulatory mechanisms controlling these cellular processes are not well understood. Here, we discuss the features of various ncRNAs, including their emerging role in contributing to biotic/abiotic stress response and plant growth and development, in addition to the molecular mechanisms involved, focusing on legume crops. Unravelling the underlying molecular mechanisms and functional implications of ncRNAs will enhance our understanding of the coordinated regulation of plant defences against various biotic and abiotic stresses and for key growth and development processes to better design various legume crops for global food security.
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MESH Headings
- Fabaceae/genetics
- Fabaceae/growth & development
- Fabaceae/metabolism
- Food Security
- Gene Expression Regulation, Developmental
- Gene Expression Regulation, Plant
- Humans
- MicroRNAs/classification
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Organ Specificity
- Protein Biosynthesis
- RNA, Circular/classification
- RNA, Circular/genetics
- RNA, Circular/metabolism
- RNA, Long Noncoding/classification
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- RNA, Plant/classification
- RNA, Plant/genetics
- RNA, Plant/metabolism
- RNA, Small Interfering/classification
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
- Species Specificity
- Stress, Physiological/genetics
- Transcription, Genetic
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Affiliation(s)
- Uday Chand Jha
- ICAR—Indian Institute of Pulses Research (IIPR), Kanpur 208024, India
- Correspondence: (U.C.J.); (K.H.M.S.)
| | - Harsh Nayyar
- Department of Botany, Panjab University, Chandigarh 160014, India;
| | - Nitin Mantri
- School of Science, RMIT University, Melbourne 3083, Australia;
| | - Kadambot H. M. Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Perth 6001, Australia
- Correspondence: (U.C.J.); (K.H.M.S.)
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Mauceri A, Abenavoli MR, Toppino L, Panda S, Mercati F, Aci MM, Aharoni A, Sunseri F, Rotino GL, Lupini A. Transcriptomics reveal new insights into molecular regulation of nitrogen use efficiency in Solanum melongena. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:4237-4253. [PMID: 33711100 DOI: 10.1093/jxb/erab121] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 03/11/2021] [Indexed: 06/12/2023]
Abstract
Nitrogen-use efficiency (NUE) is a complex trait of great interest in breeding programs because through its improvement, high crop yields can be maintained whilst N supply is reduced. In this study, we report a transcriptomic analysis of four NUE-contrasting eggplant (Solanum melongena) genotypes following short- and long-term exposure to low N, to identify key genes related to NUE in the roots and shoots. The differentially expressed genes in the high-NUE genotypes are involved in the light-harvesting complex and receptor, a ferredoxin-NADP reductase, a catalase and WRKY33. These genes were then used as bait for a co-expression gene network analysis in order to identify genes with the same trends in expression. This showed that up-regulation of WRKY33 triggered higher expression of a cluster of 21 genes and also of other genes, many of which were related to N-metabolism, that were able to improve both nitrogen uptake efficiency and nitrogen utilization efficiency, the two components of NUE. We also conducted an independent de novo experiment to validate the significantly higher expression of WRKY33 and its gene cluster in the high-NUE genotypes. Finally, examination of an Arabidopsis transgenic 35S::AtWRKY33 overexpression line showed that it had a bigger root system and was more efficient at taking up N from the soil, confirming the pivotal role of WRKY33 for NUE improvement.
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Affiliation(s)
- Antonio Mauceri
- Dipartimento Agraria, Università degli Studi Mediterranea di Reggio Calabria, Loc. Feo di Vito, Reggio Calabria, Italy
| | - Maria Rosa Abenavoli
- Dipartimento Agraria, Università degli Studi Mediterranea di Reggio Calabria, Loc. Feo di Vito, Reggio Calabria, Italy
| | - Laura Toppino
- CREA - Research Centre for Genomics and Bioinformatics, Via Paullese 28, Montanaso Lombardo, Italy
| | - Sayantan Panda
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Francesco Mercati
- Istituto di Bioscienze e Biorisorse CNR - Consiglio Nazionale Ricerche, Corso Calatafimi 414, Palermo, Italy
| | - Meriem Miyassa Aci
- Dipartimento Agraria, Università degli Studi Mediterranea di Reggio Calabria, Loc. Feo di Vito, Reggio Calabria, Italy
| | - Asaph Aharoni
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Francesco Sunseri
- Dipartimento Agraria, Università degli Studi Mediterranea di Reggio Calabria, Loc. Feo di Vito, Reggio Calabria, Italy
| | - Giuseppe Leonardo Rotino
- CREA - Research Centre for Genomics and Bioinformatics, Via Paullese 28, Montanaso Lombardo, Italy
| | - Antonio Lupini
- Dipartimento Agraria, Università degli Studi Mediterranea di Reggio Calabria, Loc. Feo di Vito, Reggio Calabria, Italy
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8
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Imran. The bioavailability of phosphorus in composite vs. hybrid maize differ with phosphorus and boron fertilization. PHOSPHORUS SULFUR 2021. [DOI: 10.1080/10426507.2021.1920588] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Imran
- Department of Agronomy, The University of Agriculture, Peshawar, Pakistan
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9
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Beleggia R, Omranian N, Holtz Y, Gioia T, Fiorani F, Nigro FM, Pecchioni N, De Vita P, Schurr U, David JL, Nikoloski Z, Papa R. Comparative Analysis Based on Transcriptomics and Metabolomics Data Reveal Differences between Emmer and Durum Wheat in Response to Nitrogen Starvation. Int J Mol Sci 2021; 22:4790. [PMID: 33946478 PMCID: PMC8124848 DOI: 10.3390/ijms22094790] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/27/2021] [Accepted: 04/28/2021] [Indexed: 12/04/2022] Open
Abstract
Mounting evidence indicates the key role of nitrogen (N) on diverse processes in plant, including development and defense. Using a combined transcriptomics and metabolomics approach, we studied the response of seedlings to N starvation of two different tetraploid wheat genotypes from the two main domesticated subspecies: emmer and durum wheat. We found that durum wheat exhibits broader and stronger response in comparison to emmer as seen from the expression pattern of both genes and metabolites and gene enrichment analysis. They showed major differences in the responses to N starvation for transcription factor families, emmer showed differential reduction in the levels of primary metabolites while durum wheat exhibited increased levels of most of them to N starvation. The correlation-based networks, including the differentially expressed genes and metabolites, revealed tighter regulation of metabolism in durum wheat in comparison to emmer. We also found that glutamate and γ-aminobutyric acid (GABA) had highest values of centrality in the metabolic correlation network, suggesting their critical role in the genotype-specific response to N starvation of emmer and durum wheat, respectively. Moreover, this finding indicates that there might be contrasting strategies associated to GABA and glutamate signaling modulating shoot vs. root growth in the two different wheat subspecies.
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Affiliation(s)
- Romina Beleggia
- Council for Agricultural Research and Economics (CREA), Research Centre for Cereal and Industrial Crops (CREA-CI), 71122 Foggia, Italy; (R.B.); (F.M.N.); (N.P.); (P.D.V.)
| | - Nooshin Omranian
- Systems Biology and Mathematical Modeling Group, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany; (N.O.); (Z.N.)
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
| | - Yan Holtz
- Montpellier SupAgro, UMR Amelioration Genetique et Adaptation des Plantes, 34060 Montpellier, France; (Y.H.); (J.L.D.)
| | - Tania Gioia
- Scuola di Scienze Agrarie, Forestali, Alimentari e Ambientali, Università degli Studi della Basilicata, 85100 Potenza, Italy;
| | - Fabio Fiorani
- Institute of Biosciences and Geosciences (IBG-2): Plant Sciences, Forschungszentrum Julich GmbH, 52428 Julich, Germany; (F.F.); (U.S.)
| | - Franca M. Nigro
- Council for Agricultural Research and Economics (CREA), Research Centre for Cereal and Industrial Crops (CREA-CI), 71122 Foggia, Italy; (R.B.); (F.M.N.); (N.P.); (P.D.V.)
| | - Nicola Pecchioni
- Council for Agricultural Research and Economics (CREA), Research Centre for Cereal and Industrial Crops (CREA-CI), 71122 Foggia, Italy; (R.B.); (F.M.N.); (N.P.); (P.D.V.)
| | - Pasquale De Vita
- Council for Agricultural Research and Economics (CREA), Research Centre for Cereal and Industrial Crops (CREA-CI), 71122 Foggia, Italy; (R.B.); (F.M.N.); (N.P.); (P.D.V.)
| | - Ulrich Schurr
- Institute of Biosciences and Geosciences (IBG-2): Plant Sciences, Forschungszentrum Julich GmbH, 52428 Julich, Germany; (F.F.); (U.S.)
| | - Jacques L. David
- Montpellier SupAgro, UMR Amelioration Genetique et Adaptation des Plantes, 34060 Montpellier, France; (Y.H.); (J.L.D.)
| | - Zoran Nikoloski
- Systems Biology and Mathematical Modeling Group, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany; (N.O.); (Z.N.)
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
- Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
| | - Roberto Papa
- Council for Agricultural Research and Economics (CREA), Research Centre for Cereal and Industrial Crops (CREA-CI), 71122 Foggia, Italy; (R.B.); (F.M.N.); (N.P.); (P.D.V.)
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università Politecnica delle Marche, 60131 Ancona, Italy
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10
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The SV, Snyder R, Tegeder M. Targeting Nitrogen Metabolism and Transport Processes to Improve Plant Nitrogen Use Efficiency. FRONTIERS IN PLANT SCIENCE 2021; 11:628366. [PMID: 33732269 PMCID: PMC7957077 DOI: 10.3389/fpls.2020.628366] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 12/31/2020] [Indexed: 05/22/2023]
Abstract
In agricultural cropping systems, relatively large amounts of nitrogen (N) are applied for plant growth and development, and to achieve high yields. However, with increasing N application, plant N use efficiency generally decreases, which results in losses of N into the environment and subsequently detrimental consequences for both ecosystems and human health. A strategy for reducing N input and environmental losses while maintaining or increasing plant performance is the development of crops that effectively obtain, distribute, and utilize the available N. Generally, N is acquired from the soil in the inorganic forms of nitrate or ammonium and assimilated in roots or leaves as amino acids. The amino acids may be used within the source organs, but they are also the principal N compounds transported from source to sink in support of metabolism and growth. N uptake, synthesis of amino acids, and their partitioning within sources and toward sinks, as well as N utilization within sinks represent potential bottlenecks in the effective use of N for vegetative and reproductive growth. This review addresses recent discoveries in N metabolism and transport and their relevance for improving N use efficiency under high and low N conditions.
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Affiliation(s)
| | | | - Mechthild Tegeder
- School of Biological Sciences, Washington State University, Pullman, WA, United States
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11
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Jha UC, Nayyar H, Jha R, Khurshid M, Zhou M, Mantri N, Siddique KHM. Long non-coding RNAs: emerging players regulating plant abiotic stress response and adaptation. BMC PLANT BIOLOGY 2020; 20:466. [PMID: 33046001 PMCID: PMC7549229 DOI: 10.1186/s12870-020-02595-x] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 08/12/2020] [Indexed: 05/13/2023]
Abstract
BACKGROUND The immobile nature of plants means that they can be frequently confronted by various biotic and abiotic stresses during their lifecycle. Among the various abiotic stresses, water stress, temperature extremities, salinity, and heavy metal toxicity are the major abiotic stresses challenging overall plant growth. Plants have evolved complex molecular mechanisms to adapt under the given abiotic stresses. Long non-coding RNAs (lncRNAs)-a diverse class of RNAs that contain > 200 nucleotides(nt)-play an essential role in plant adaptation to various abiotic stresses. RESULTS LncRNAs play a significant role as 'biological regulators' for various developmental processes and biotic and abiotic stress responses in animals and plants at the transcription, post-transcription, and epigenetic level, targeting various stress-responsive mRNAs, regulatory gene(s) encoding transcription factors, and numerous microRNAs (miRNAs) that regulate the expression of different genes. However, the mechanistic role of lncRNAs at the molecular level, and possible target gene(s) contributing to plant abiotic stress response and adaptation, remain largely unknown. Here, we review various types of lncRNAs found in different plant species, with a focus on understanding the complex molecular mechanisms that contribute to abiotic stress tolerance in plants. We start by discussing the biogenesis, type and function, phylogenetic relationships, and sequence conservation of lncRNAs. Next, we review the role of lncRNAs controlling various abiotic stresses, including drought, heat, cold, heavy metal toxicity, and nutrient deficiency, with relevant examples from various plant species. Lastly, we briefly discuss the various lncRNA databases and the role of bioinformatics for predicting the structural and functional annotation of novel lncRNAs. CONCLUSIONS Understanding the intricate molecular mechanisms of stress-responsive lncRNAs is in its infancy. The availability of a comprehensive atlas of lncRNAs across whole genomes in crop plants, coupled with a comprehensive understanding of the complex molecular mechanisms that regulate various abiotic stress responses, will enable us to use lncRNAs as potential biomarkers for tailoring abiotic stress-tolerant plants in the future.
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Affiliation(s)
- Uday Chand Jha
- ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, 208024, India.
| | - Harsh Nayyar
- Department of Botany, Panjab University, Chandigarh, India
| | - Rintu Jha
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Muhammad Khurshid
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Institute of Biochemistry and Biotechnology, University of the Punjab, Lahore, Pakistan
| | - Meiliang Zhou
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Nitin Mantri
- School of Science, RMIT University, Plenty Road, Bundoora. Victoria. 3083., Australia
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6001, Australia.
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12
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Gong X, Liu X, Pan Q, Mi G, Chen F, Yuan L. Combined physiological, transcriptome, and genetic analysis reveals a molecular network of nitrogen remobilization in maize. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5061-5073. [PMID: 32392584 DOI: 10.1093/jxb/eraa229] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 05/06/2020] [Indexed: 05/28/2023]
Abstract
In plants, nitrogen remobilization from source to sink organs is an important process regulated by complex transcriptional regulatory networks. However, the relationship between nitrogen remobilization and leaf senescence and the molecular regulatory network that controls them are unknown in maize. Here, using 15N labeling and a transcriptome approach, a dynamic analysis of the nitrogen remobilization process was conducted in two elite maize inbred lines (PH4CV and PH6WC) with contrasting leaf senescence. PH4CV showed higher nitrogen remobilization efficiency (NRE) than PH6WC, mainly in the middle and lower leaves from 15 d to 35 d after silking. The co-expression network analysis revealed that ethylene and cytokinin metabolism-related genes triggered the onset of nitrogen remobilization, while abscisic acid and jasmonic acid biosynthesis-related genes controlled the progression of nitrogen remobilization. By integrating genetic analysis, functional annotation, and gene expression, two candidate genes underlying a major quantitative trait locus of NRE were identified, namely an early senescence acting gene (ZmASR6) and an ATP-dependent Clp protease gene (GRMZM2G172230). Hormone-coupled transcription factors and downstream target genes reveal a gene regulatory network for the nitrogen remobilization process after silking in maize. These results uncovered a sophisticated regulatory mechanism for nitrogen remobilization, and further provided characterization of valuable genes for genetic improvement of nitrogen use efficiency in maize.
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Affiliation(s)
- Xiaoping Gong
- College of Resources and Environmental Sciences; National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions of MOE, China Agricultural University, Beijing, China
| | - Xiaoyang Liu
- College of Resources and Environmental Sciences; National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions of MOE, China Agricultural University, Beijing, China
| | - Qingchun Pan
- College of Resources and Environmental Sciences; National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions of MOE, China Agricultural University, Beijing, China
| | - Guohua Mi
- College of Resources and Environmental Sciences; National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions of MOE, China Agricultural University, Beijing, China
| | - Fanjun Chen
- College of Resources and Environmental Sciences; National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions of MOE, China Agricultural University, Beijing, China
| | - Lixing Yuan
- College of Resources and Environmental Sciences; National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions of MOE, China Agricultural University, Beijing, China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, China
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13
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Schroeder WL, Saha R. Introducing an Optimization- and explicit Runge-Kutta- based Approach to Perform Dynamic Flux Balance Analysis. Sci Rep 2020; 10:9241. [PMID: 32514037 PMCID: PMC7280247 DOI: 10.1038/s41598-020-65457-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 05/04/2020] [Indexed: 11/17/2022] Open
Abstract
In this work we introduce the generalized Optimization- and explicit Runge-Kutta-based Approach (ORKA) to perform dynamic Flux Balance Analysis (dFBA), which is numerically more accurate and computationally tractable than existing approaches. ORKA is applied to a four-tissue (leaf, root, seed, and stem) model of Arabidopsis thaliana, p-ath773, uniquely capturing the core-metabolism of several stages of growth from seedling to senescence at hourly intervals. Model p-ath773 has been designed to show broad agreement with published plant-scale properties such as mass, maintenance, and senescence, yet leaving reaction-level behavior unconstrainted. Hence, it serves as a framework to study the reaction-level behavior necessary for observed plant-scale behavior. Two such case studies of reaction-level behavior include the lifecycle progression of sulfur metabolism and the diurnal flow of water throughout the plant. Specifically, p-ath773 shows how transpiration drives water flow through the plant and how water produced by leaf tissue metabolism may contribute significantly to transpired water. Investigation of sulfur metabolism elucidates frequent cross-compartment exchange of a standing pool of amino acids which is used to regulate the proton flow. Overall, p-ath773 and ORKA serve as scaffolds for dFBA-based lifecycle modeling of plants and other systems to further broaden the scope of in silico metabolic investigation.
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Affiliation(s)
- Wheaton L Schroeder
- Department of Chemical and Biomolecular Engineering, University of Nebraska - Lincoln, Lincoln, USA
| | - Rajib Saha
- Department of Chemical and Biomolecular Engineering, University of Nebraska - Lincoln, Lincoln, USA.
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14
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Tucker SL, Dohleman FG, Grapov D, Flagel L, Yang S, Wegener KM, Kosola K, Swarup S, Rapp RA, Bedair M, Halls SC, Glenn KC, Hall MA, Allen E, Rice EA. Evaluating maize phenotypic variance, heritability, and yield relationships at multiple biological scales across agronomically relevant environments. PLANT, CELL & ENVIRONMENT 2020; 43:880-902. [PMID: 31733168 DOI: 10.1111/pce.13681] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 11/04/2019] [Accepted: 11/11/2019] [Indexed: 05/22/2023]
Abstract
A challenge to improve an integrative phenotype, like yield, is the interaction between the broad range of possible molecular and physiological traits that contribute to yield and the multitude of potential environmental conditions in which they are expressed. This study collected data on 31 phenotypic traits, 83 annotated metabolites, and nearly 22,000 transcripts from a set of 57 diverse, commercially relevant maize hybrids across three years in central U.S. Corn Belt environments. Although variability in characteristics created a complex picture of how traits interact produce yield, phenotypic traits and gene expression were more consistent across environments, while metabolite levels showed low repeatability. Phenology traits, such as green leaf number and grain moisture and whole plant nitrogen content showed the most consistent correlation with yield. A machine learning predictive analysis of phenotypic traits revealed that ear traits, phenology, and root traits were most important to predicting yield. Analysis suggested little correlation between biomass traits and yield, suggesting there is more of a sink limitation to yield under the conditions studied here. This work suggests that continued improvement of maize yields requires a strong understanding of baseline variation of plant characteristics across commercially-relevant germplasm to drive strategies for consistently improving yield.
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Affiliation(s)
| | | | | | - Lex Flagel
- Bayer Crop Science, Chesterfield, Missouri
| | - Sean Yang
- Bayer Crop Science, Chesterfield, Missouri
| | | | | | | | - Ryan A Rapp
- Pairwise, Research Triangle Park, North Carolina
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15
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Sun CX, Hao L, Wang D, Li C, Zhang C, Chen X, Fu J, Zhang YL. Nitrogen utilisation and metabolism in maize (Zea mays L.) plants under different rates of biochar addition and nitrogen input conditions. PLANT BIOLOGY (STUTTGART, GERMANY) 2019; 21:882-890. [PMID: 31002433 DOI: 10.1111/plb.12997] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 04/11/2019] [Indexed: 05/26/2023]
Abstract
Biochar (BC) application could improve plant nitrogen (N) utilisation and potentially reduce N fertiliser requirements. However, the fate of N in crop-soil systems and the metabolic responses of crops under conditions of BC co-applied with reduced N are not well understood. The urea-15 N isotope and pot experiments with three BC rates (0%, 5% and 15%; w/w) combined with three N fertiliser levels (100% N, 85% N and 55% N) were conducted for maize. The metabolome, 15 N abundance and gene expression in plants were analysed using nuclear magnetic resonance, gas isotope mass spectrometry and quantitative real-time reverse transcription PCR, respectively. The results showed that recovery of N by maize ranged from 27.4% to 23.6% and decreased as the N application rate decreased (from 100% to 55%) without BC addition, but ranged from 24.6% to 29.4% when BC was added at a rate of 5% and increased as the N application rate decreased. BC addition had major effects on global metabolic profiles and metabolic networks at the metabolomics level as well as on the expression of related genes (zmGS1and zmAS1) and the content of mineral N (NO3 - , NO2 - and NH4 + ) in maize seedlings; moreover, the interaction effects of the BC application rates and N fertiliser levels were evident (P ≤ 0.001). BC addition induced a decrease in the flux toward sugar hydrolysis and maintained homeostasis in the amino acid pool, which was perturbed by reduced N levels; after which the maize plants adapted to the reduced N condition, and the N recovery efficiency ultimately improved with reduced N loss.
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Affiliation(s)
- C X Sun
- College of Life and Health Sciences, Northeastern University, Shenyang, Liaoning Province, China
| | - L Hao
- College of Life and Health Sciences, Northeastern University, Shenyang, Liaoning Province, China
| | - D Wang
- College of Life and Health Sciences, Northeastern University, Shenyang, Liaoning Province, China
| | - C Li
- College of Life and Health Sciences, Northeastern University, Shenyang, Liaoning Province, China
| | - C Zhang
- College of Life and Health Sciences, Northeastern University, Shenyang, Liaoning Province, China
| | - X Chen
- College of Life and Health Sciences, Northeastern University, Shenyang, Liaoning Province, China
| | - J Fu
- College of Life and Health Sciences, Northeastern University, Shenyang, Liaoning Province, China
| | - Y L Zhang
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning Province, China
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16
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Song H, Cai Z, Liao J, Tang D, Zhang S. Sexually differential gene expressions in poplar roots in response to nitrogen deficiency. TREE PHYSIOLOGY 2019; 39:1614-1629. [PMID: 31115478 DOI: 10.1093/treephys/tpz057] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Revised: 04/13/2019] [Accepted: 05/10/2019] [Indexed: 05/27/2023]
Abstract
Nitrogen (N) is a key nutrient impacting plant growth and physiological processes. However, the supply of N is often not sufficient to meet the requirements of trees in many terrestrial ecosystems. Because of differences in production costs, male and female plants have evolved different stress resistance strategies for N limitation. However, little is known about differential gene expression according to sex in poplars responding to N limitation. To explore sex-related constitutive defenses, Populus cathayana Rehder transcriptomic, proteomic and metabolic analyses were performed on the roots of male and female Populus cathayana. We detected 16,816 proteins and 37,286 transcripts, with 2797 overlapping proteins and mRNAs in the roots. In combination with the identification of 90 metabolites, we found that N deficiency greatly altered gene expression related to N metabolism as well as carbohydrate metabolism, secondary metabolism and stress-related processes in both sexes. Nitrogen-deficient P. cathayana females exhibited greater root biomass and less inhibition of citric acid production and glycolysis as well as higher secondary metabolic activity and abscisic acid contents than N-deficient P. cathayana males. Interestingly, males presented a better osmotic adjustment ability and higher expression of resistance genes, suggesting that P. cathayana males exhibit a better stress tolerance ability and can invest fewer resources in defense compared with females. Therefore, our study provides new molecular evidence that P. cathayana males and females adopt different resistance strategies to cope with N deficiency in their roots.
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Affiliation(s)
- Haifeng Song
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu, China
- Key Laboratory of Mountain Surface Processes and Ecological Regulation, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zeyu Cai
- Key Laboratory of Mountain Surface Processes and Ecological Regulation, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jun Liao
- Key Laboratory of Mountain Surface Processes and Ecological Regulation, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Duoteng Tang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu, China
| | - Sheng Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu, China
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17
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Zeffa DM, Perini LJ, Silva MB, de Sousa NV, Scapim CA, de Oliveira ALM, do Amaral Júnior AT, Azeredo Gonçalves LS. Azospirillum brasilense promotes increases in growth and nitrogen use efficiency of maize genotypes. PLoS One 2019; 14:e0215332. [PMID: 30998695 PMCID: PMC6472877 DOI: 10.1371/journal.pone.0215332] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 03/29/2019] [Indexed: 11/19/2022] Open
Abstract
The development of cultivars with an improved nitrogen use efficiency (NUE) together with the application of plant growth-promoting bacteria is considered one of the main strategies for reduction of fertilizers use. In this sense, this study: i) evaluated the effect of Azospirillum brasilense on the initial development of maize genotypes; ii) investigated the influence of A. brasilense inoculation on NUE under nitrogen deficit; and iii) sought for more NUE genotypes with higher responsiveness to A. brasilense inoculation. Twenty-seven maize genotypes were evaluated in three independent experiments. The first evaluated the initial development of maize genotypes with and without A. brasilense (strain Ab-V5) inoculation of seeds on germination paper in a growth chamber. The second and third experiments were carried out in a greenhouse using Leonard pots and pots with substrate, respectively, and the genotypes were evaluated at high nitrogen, low nitrogen and low nitrogen plus A. brasilense Ab-V5 inoculation. The inoculation of seeds with A. brasilense Ab-V5 intensified plant growth, improved biochemical traits and raised NUE under nitrogen deficit. The inoculation of seeds with A. brasilense can be considered an economically viable and environmentally sustainable strategy for maize cultivation.
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Affiliation(s)
| | - Luiz Júnior Perini
- Department of Agronomy, Universidade Estadual de Londrina, Londrina, Paraná, Brazil
| | - Mayara Barbosa Silva
- Department of Agronomy, Universidade Estadual de Maringá, Maringá, Paraná, Brazil
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18
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Nigro D, Gadaleta A, Mangini G, Colasuonno P, Marcotuli I, Giancaspro A, Giove SL, Simeone R, Blanco A. Candidate genes and genome-wide association study of grain protein content and protein deviation in durum wheat. PLANTA 2019; 249:1157-1175. [PMID: 30603787 DOI: 10.1007/s00425-018-03075-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 12/19/2018] [Indexed: 05/26/2023]
Abstract
Stable QTL for grain protein content co-migrating with nitrogen-related genes have been identified by the candidate genes and genome-wide association mapping approaches useful for marker-assisted selection. Grain protein content (GPC) is one of the most important quality traits in wheat, defining the nutritional and end-use properties and rheological characteristics. Over the years, a number of breeding programs have been developed aimed to improving GPC, most of them having been prevented by the negative correlation with grain yield. To overcome this issue, a collection of durum wheat germplasm was evaluated for both GPC and grain protein deviation (GPD) in seven field trials. Fourteen candidate genes involved in several processes related to nitrogen metabolism were precisely located on two high-density consensus maps of common and durum wheat, and six of them were found to be highly associated with both traits. The wheat collection was genotyped using the 90 K iSelect array, and 11 stable quantitative trait loci (QTL) for GPC were detected in at least three environments and the mean across environments by the genome-wide association mapping. Interestingly, seven QTL were co-migrating with N-related candidate genes. Four QTL were found to be significantly associated to increases of GPD, indicating that selecting for GPC could not affect final grain yield per spike. The combined approaches of candidate genes and genome-wide association mapping led to a better understanding of the genetic relationships between grain storage proteins and grain yield per spike, and provided useful information for marker-assisted selection programs.
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Affiliation(s)
- D Nigro
- Department of Soil, Plant and Food Sciences, Genetics and Plant Breeding Section, University of Bari, Bari, Italy
| | - A Gadaleta
- Department of Agricultural and Environmental Science, Research Unit of "Genetics and Plant Biotechnology", University of Bari, Bari, Italy.
| | - G Mangini
- Department of Soil, Plant and Food Sciences, Genetics and Plant Breeding Section, University of Bari, Bari, Italy
| | - P Colasuonno
- Department of Agricultural and Environmental Science, Research Unit of "Genetics and Plant Biotechnology", University of Bari, Bari, Italy
| | - I Marcotuli
- Department of Agricultural and Environmental Science, Research Unit of "Genetics and Plant Biotechnology", University of Bari, Bari, Italy
| | - A Giancaspro
- Department of Agricultural and Environmental Science, Research Unit of "Genetics and Plant Biotechnology", University of Bari, Bari, Italy
| | - S L Giove
- Department of Agricultural and Environmental Science, Research Unit of "Genetics and Plant Biotechnology", University of Bari, Bari, Italy
| | - R Simeone
- Department of Soil, Plant and Food Sciences, Genetics and Plant Breeding Section, University of Bari, Bari, Italy
| | - A Blanco
- Department of Soil, Plant and Food Sciences, Genetics and Plant Breeding Section, University of Bari, Bari, Italy
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19
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Cukier C, Lea PJ, Cañas R, Marmagne A, Limami AM, Hirel B. Labeling Maize (Zea mays L.) Leaves with 15 NH 4+ and Monitoring Nitrogen Incorporation into Amino Acids by GC/MS Analysis. ACTA ACUST UNITED AC 2018; 3:e20073. [PMID: 30198634 DOI: 10.1002/cppb.20073] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The human body contains approximately 3.2% nitrogen (N), mainly present as protein and amino acids. Although N exists at a high concentration (78%) in the air, it is not readily available to animals and most plants. Plants are however able to take up both nitrate (NO3- ) and ammonium (NH4+ ) ions from the soil and convert them to amino acids and proteins, which are excellent sources for all animals. Most N is available as the stable isotope 14 N, but a second form, 15 N, is present in very low concentrations. 15 N can be detected in extracts of plants by gas chromatography followed by mass spectrometry (GC/MS). In this protocol, the methods are described for tracing the pathway by which plants are able to take up 15 N-labeled nitrate and ammonium and convert them into amino acids and proteins. A protocol for extracting and quantifying amino acids and 15 N enrichment in maize (Zea mays L.) leaves labeled with 15 NH4+ is described. Following amino acid extraction, purification, and separation by GC/MS, a calculation of the 15 N enrichment of each amino acid is carried out on a relative basis to identify any differences in the dynamics of amino acid accumulation. This will allow a study of the impact of genetic modifications or mutations on key reactions involved in primary nitrogen and carbon metabolism. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Caroline Cukier
- University of Angers, Institut de Recherche en Horticulture et Semences (IRHS), INRA, Angers, France
| | - Peter J Lea
- Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, United Kingdom
| | - Rafael Cañas
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
| | - Anne Marmagne
- Institut Jean-Pierre Bourgin, INRA, Agro-ParisTech, Université de Paris-Saclay, Versailles, France
| | - Anis M Limami
- University of Angers, Institut de Recherche en Horticulture et Semences (IRHS), INRA, Angers, France
| | - Bertrand Hirel
- Institut Jean-Pierre Bourgin, INRA, Agro-ParisTech, Université de Paris-Saclay, Versailles, France
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20
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Tiwari JK, Plett D, Garnett T, Chakrabarti SK, Singh RK. Integrated genomics, physiology and breeding approaches for improving nitrogen use efficiency in potato: translating knowledge from other crops. FUNCTIONAL PLANT BIOLOGY : FPB 2018; 45:587-605. [PMID: 32290962 DOI: 10.1071/fp17303] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 12/06/2017] [Indexed: 05/22/2023]
Abstract
Potato plays a key role in global food and nutritional security. Potato is an N fertiliser-responsive crop, producing high tuber yields. However, excessive use of N can result in environmental damage and high production costs, hence improving nitrogen use efficiency (NUE) of potato plants is one of the sustainable options to address these issues and increase yield. Advanced efforts have been undertaken to improve NUE in other plants like Arabidopsis, rice, wheat and maize through molecular and physiological approaches. Conversely, in potato, NUE studies have predominantly focussed on agronomy or soil management, except for a few researchers who have measured gene expression and proteins relevant to N uptake or metabolism. The focus of this review is to adapt knowledge gained from other plants to inform investigation of N metabolism and associated traits in potato with the aim of improving potato NUE using integrated genomics, physiology and breeding methods.
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Affiliation(s)
- Jagesh K Tiwari
- ICAR-Central Potato Research Institute, Shimla - 171001, Himachal Pradesh, India
| | - Darren Plett
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, SA 5064, Australia
| | - Trevor Garnett
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, SA 5064, Australia
| | - Swarup K Chakrabarti
- ICAR-Central Potato Research Institute, Shimla - 171001, Himachal Pradesh, India
| | - Rajesh K Singh
- ICAR-Central Potato Research Institute, Shimla - 171001, Himachal Pradesh, India
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21
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Duval BD, Ghimire R, Hartman MD, Marsalis MA. Water and nitrogen management effects on semiarid sorghum production and soil trace gas flux under future climate. PLoS One 2018; 13:e0195782. [PMID: 29672548 PMCID: PMC5908084 DOI: 10.1371/journal.pone.0195782] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 03/29/2018] [Indexed: 11/18/2022] Open
Abstract
External inputs to agricultural systems can overcome latent soil and climate constraints on production, while contributing to greenhouse gas emissions from fertilizer and water management inefficiencies. Proper crop selection for a given region can lessen the need for irrigation and timing of N fertilizer application with crop N demand can potentially reduce N2O emissions and increase N use efficiency while reducing residual soil N and N leaching. However, increased variability in precipitation is an expectation of climate change and makes predicting biomass and gas flux responses to management more challenging. We used the DayCent model to test hypotheses about input intensity controls on sorghum (Sorghum bicolor (L.) Moench) productivity and greenhouse gas emissions in the southwestern United States under future climate. Sorghum had been previously parameterized for DayCent, but an inverse-modeling via parameter estimation method significantly improved model validation to field data. Aboveground production and N2O flux were more responsive to N additions than irrigation, but simulations with future climate produced lower values for sorghum than current climate. We found positive interactions between irrigation at increased N application for N2O and CO2 fluxes. Extremes in sorghum production under future climate were a function of biomass accumulation trajectories related to daily soil water and mineral N. Root C inputs correlated with soil organic C pools, but overall soil C declined at the decadal scale under current weather while modest gains were simulated under future weather. Scaling biomass and N2O fluxes by unit N and water input revealed that sorghum can be productive without irrigation, and the effect of irrigating crops is difficult to forecast when precipitation is variable within the growing season. These simulation results demonstrate the importance of understanding sorghum production and greenhouse gas emissions at daily scales when assessing annual and decadal-scale management decisions’ effects on aspects of arid and semiarid agroecosystem biogeochemistry.
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Affiliation(s)
- Benjamin D. Duval
- Department of Biology, New Mexico Institute of Mining and Technology, Socorro, NM, United States of America
- * E-mail:
| | - Rajan Ghimire
- New Mexico State University, Agricultural Science Center, Clovis, New Mexico, United States of America
| | - Melannie D. Hartman
- Natural Resource Ecology Laboratory, Colorado State University, Fort Collins, Colorado, United States of America
| | - Mark A. Marsalis
- New Mexico State University, Agricultural Science Center, Los Lunas, New Mexico, United States of America
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22
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The cyanobacterial ornithine-ammonia cycle involves an arginine dihydrolase. Nat Chem Biol 2018; 14:575-581. [PMID: 29632414 DOI: 10.1038/s41589-018-0038-z] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 02/23/2018] [Indexed: 11/09/2022]
Abstract
Living organisms have evolved mechanisms for adjusting their metabolism to adapt to environmental nutrient availability. Terrestrial animals utilize the ornithine-urea cycle to dispose of excess nitrogen derived from dietary protein. Here, we identified an active ornithine-ammonia cycle (OAC) in cyanobacteria through an approach combining dynamic 15N and 13C tracers, metabolomics, and mathematical modeling. The pathway starts with carbamoyl phosphate synthesis by the bacterial- and plant-type glutamine-dependent enzyme and ends with conversion of arginine to ornithine and ammonia by a novel arginine dihydrolase. An arginine dihydrolase-deficient mutant showed disruption of OAC and severely impaired cell growth when nitrogen availability oscillated. We demonstrated that the OAC allows for rapid remobilization of nitrogen reserves under starvation and a high rate of nitrogen assimilation and storage after the nutrient becomes available. Thus, the OAC serves as a conduit in the nitrogen storage-and-remobilization machinery in cyanobacteria and enables cellular adaptation to nitrogen fluctuations.
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23
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Dechorgnat J, Francis KL, Dhugga KS, Rafalski JA, Tyerman SD, Kaiser BN. Root Ideotype Influences Nitrogen Transport and Assimilation in Maize. FRONTIERS IN PLANT SCIENCE 2018; 9:531. [PMID: 29740466 PMCID: PMC5928562 DOI: 10.3389/fpls.2018.00531] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 04/05/2018] [Indexed: 05/02/2023]
Abstract
Maize (Zea mays, L.) yield is strongly influenced by external nitrogen inputs and their availability in the soil solution. Overuse of nitrogen-fertilizers can have detrimental ecological consequences through increased nitrogen pollution of water and the release of the potent greenhouse gas, nitrous oxide. To improve yield and overall nitrogen use efficiency (NUE), a deeper understanding of nitrogen uptake and utilization is required. This study examines the performance of two contrasting maize inbred lines, B73 and F44. F44 was selected in Florida on predominantly sandy acidic soils subject to nitrate leaching while B73 was selected in Iowa on rich mollisol soils. Transcriptional, enzymatic and nitrogen transport analytical tools were used to identify differences in their N absorption and utilization capabilities. Our results show that B73 and F44 differ significantly in their genetic, enzymatic, and biochemical root nitrogen transport and assimilatory pathways. The phenotypes show a strong genetic relationship linked to nitrogen form, where B73 showed a greater capacity for ammonium transport and assimilation whereas F44 preferred nitrate. The contrasting phenotypes are typified by differences in root system architecture (RSA) developed in the presence of both nitrate and ammonium. F44 crown roots were longer, had a higher surface area and volume with a greater lateral root number and density than B73. In contrast, B73 roots (primary, seminal, and crown) were more abundant but lacked the defining features of the F44 crown roots. An F1 hybrid between B73 and F44 mirrored the B73 nitrogen specificity and root architecture phenotypes, indicating complete dominance of the B73 inbred. This study highlights the important link between RSA and nitrogen management and why both variables need to be tested together when defining NUE improvements in any selection program.
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Affiliation(s)
- Julie Dechorgnat
- Sydney Institute of Agriculture, School of Life and Environmental Sciences, The University of Sydney, Camden, NSW, Australia
| | - Karen L. Francis
- School of Agriculture, Food and Wine, The University of Adelaide, Urrbrae, SA, Australia
| | | | - J. A. Rafalski
- Genetic Discovery Group, DuPont Crop Genetics Research, DuPont Experimental Station, Wilmington, DE, United States
| | - Stephen D. Tyerman
- School of Agriculture, Food and Wine, The University of Adelaide, Urrbrae, SA, Australia
| | - Brent N. Kaiser
- Sydney Institute of Agriculture, School of Life and Environmental Sciences, The University of Sydney, Camden, NSW, Australia
- *Correspondence: Brent N. Kaiser,
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24
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Fan TF, He MJ, Li CJ, Shi DX, Yang C, Chen YY, Ke J, Chen YX, Zhang L, Li DQ, Liu LH, Xu C. Physiological dissection revealed that both uptake and assimilation are the major components regulating different growth responses of two tobacco cultivars to nitrogen nutrition. PLANT BIOLOGY (STUTTGART, GERMANY) 2018; 20:39-49. [PMID: 28985445 DOI: 10.1111/plb.12642] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Accepted: 09/30/2017] [Indexed: 06/07/2023]
Abstract
K326 and HD represent major tobacco cultivars in China, which required large N fertiliser input but at different application rates. To understand primary components affecting tobacco N use physiology, we adopted these two varieties as valuable genetic material to assess their growth response to N nutrition. We established a hydroponic culture system to grow plants supplied with different N regimes. Plant biomass, N, ammonium, nitrate, arginine, GS and NR activity, N transfer and use efficiency as well as root uptake were examined. Our data revealed the preference of K326 and HD to utilise nitrate or ammonium nitrate but not ammonium alone, with 2 mm N supply probably sufficient and economical to achieve good biomass production at the vegetative stage. Moreover, both varieties were very sensitive to ammonium, perhaps due to lack of or abnormal signalling related to nitrate and/or arginine rather than impairment of N acquisition and initial assimilation; this was supported by measurements of the plant content of N, ammonium and activities of GS and NR. Notably, short-term 15 N root influx studies identified differential uptake kinetics of K326 and HD, with distinct affinities and transport rates for ammonium and nitrate. The data suggest that the growth adaptation of K326 or HD to higher or lower N may be ascribed to different competences for effective N uptake/translocation and assimilation. Thus, our work provides valuable information to prompt deeper investigation of the molecular basis controlling plant N use efficiency.
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Affiliation(s)
- T-F Fan
- Institute of Chongqing Tobacco Science Research of Chongqing Tobacco Company, China Tobacco Corporation, Chongqing, China
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - M-J He
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
- College of Agriculture Sciences, Hunan Agricultural University, Changsha, China
| | - C-J Li
- Institute of Chongqing Tobacco Science Research of Chongqing Tobacco Company, China Tobacco Corporation, Chongqing, China
| | - D-X Shi
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - C Yang
- Institute of Chongqing Tobacco Science Research of Chongqing Tobacco Company, China Tobacco Corporation, Chongqing, China
| | - Y-Y Chen
- Institute of Chongqing Tobacco Science Research of Chongqing Tobacco Company, China Tobacco Corporation, Chongqing, China
| | - J Ke
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Y-X Chen
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - L Zhang
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - D-Q Li
- College of Agriculture Sciences, Hunan Agricultural University, Changsha, China
| | - L-H Liu
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
- College of Agriculture Sciences, Hunan Agricultural University, Changsha, China
| | - C Xu
- Institute of Chongqing Tobacco Science Research of Chongqing Tobacco Company, China Tobacco Corporation, Chongqing, China
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25
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Li G, Wu Y, Liu G, Xiao X, Wang P, Gao T, Xu M, Han Q, Wang Y, Guo T, Kang G. Large-scale Proteomics Combined with Transgenic Experiments Demonstrates An Important Role of Jasmonic Acid in Potassium Deficiency Response in Wheat and Rice. Mol Cell Proteomics 2017; 16:1889-1905. [PMID: 28821602 PMCID: PMC5671998 DOI: 10.1074/mcp.ra117.000032] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Indexed: 12/03/2022] Open
Abstract
Potassium (K+) is the most abundant inorganic cation in plants, and molecular dissection of K+ deficiency has received considerable interest in order to minimize K+ fertilizer input and develop high quality K+-efficient crops. However, the molecular mechanism of plant responses to K+ deficiency is still poorly understood. In this study, 2-week-old bread wheat seedlings grown hydroponically in Hoagland solution were transferred to K+-free conditions for 8 d, and their root and leaf proteome profiles were assessed using the iTRAQ proteome method. Over 4000 unique proteins were identified, and 818 K+-responsive protein species showed significant differences in abundance. The differentially expressed protein species were associated with diverse functions and exhibited organ-specific differences. Most of the differentially expressed protein species related to hormone synthesis were involved in jasmonic acid (JA) synthesis and the upregulated abundance of JA synthesis-related enzymes could result in the increased JA concentrations. Abundance of allene oxide synthase (AOS), one key JA synthesis-related enzyme, was significantly increased in K+-deficient wheat seedlings, and its overexpression markedly increased concentrations of K+ and JA, altered the transcription levels of some genes encoding K+-responsive protein species, as well as enhanced the tolerance of rice plants to low K+ or K+ deficiency. Moreover, rice AOS mutant (osaos) exhibited more sensitivity to low K+ or K+ deficiency. Our findings could highlight the importance of JA in K+ deficiency, and imply a network of molecular processes underlying plant responses to K+ deficiency.
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Affiliation(s)
- Gezi Li
- From the ‡National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, 450002, China.,§Collaborative Innovation Center of Henan Food Crops, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yufang Wu
- From the ‡National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, 450002, China
| | - Guoyu Liu
- From the ‡National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, 450002, China
| | - Xianghong Xiao
- §Collaborative Innovation Center of Henan Food Crops, Henan Agricultural University, Zhengzhou, 450002, China
| | - Pengfei Wang
- From the ‡National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, 450002, China
| | - Tian Gao
- From the ‡National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, 450002, China
| | - Mengjun Xu
- §Collaborative Innovation Center of Henan Food Crops, Henan Agricultural University, Zhengzhou, 450002, China
| | - Qiaoxia Han
- ¶National Engineering Research Centre for Wheat, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yonghua Wang
- From the ‡National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, 450002, China.,¶National Engineering Research Centre for Wheat, Henan Agricultural University, Zhengzhou, 450002, China
| | - Tiancai Guo
- From the ‡National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, 450002, China.,¶National Engineering Research Centre for Wheat, Henan Agricultural University, Zhengzhou, 450002, China
| | - Guozhang Kang
- From the ‡National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, 450002, China; .,§Collaborative Innovation Center of Henan Food Crops, Henan Agricultural University, Zhengzhou, 450002, China
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Gomes de Oliveira Dal'Molin C, Nielsen LK. Plant genome-scale reconstruction: from single cell to multi-tissue modelling and omics analyses. Curr Opin Biotechnol 2017; 49:42-48. [PMID: 28806583 DOI: 10.1016/j.copbio.2017.07.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 07/17/2017] [Accepted: 07/17/2017] [Indexed: 10/25/2022]
Abstract
In this review, we present the latest developments in plant systems biology with particular emphasis on plant genome-scale reconstructions and multi-omics analyses. Understanding multicellular metabolism is far from trivial and 'omics' data are difficult to interpret in the absence of a systems framework. 'Omics' data appropriately integrated with genome-scale reconstructions and modelling facilitates our understanding of how individual components interact and influence overall cell, tissue or organisms function. Here we present examples of how plant metabolic reconstructions and modelling are used as a systems-based framework for improving our understanding of the plant metabolic processes in single cells and multiple tissues.
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Affiliation(s)
| | - Lars Keld Nielsen
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, Queensland 4072, Australia.
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27
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Liu F, Xiang N, Hu JG, Shijuan Y, Xie L, Brennan CS, Huang W, Guo X. The manipulation of gene expression and the biosynthesis of Vitamin C, E and folate in light-and dark-germination of sweet corn seeds. Sci Rep 2017; 7:7484. [PMID: 28790401 PMCID: PMC5548755 DOI: 10.1038/s41598-017-07774-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 07/03/2017] [Indexed: 11/09/2022] Open
Abstract
This study investigates the potential interrelationship between gene expression and biosynthesis of vitamin C, E and folate in sweet corn sprouts. Germination of sweet corn kernels was conducted in light and dark environments to determine if this relationship was regulated by photo-illumination. Results indicated that light and dark environments affected the DHAR, TMT and GTPCH expression and that these genes were the predominant genes of vitamin C, E and folate biosynthesis pathways respectively during the germination. Levels of vitamin C and folate increased during the germination of sweet corn seeds while vitamin E had a declining manner. Sweet corn sprouts had higher vitamin C and E levels as well as relevant gene expression levels in light environment while illumination had little influence on the folate contents and the gene expression levels during the germination. These results indicate that there might be a collaborative relationship between vitamin C and folate regulation during sweet corn seed germination, while an inhibitive regulation might exist between vitamin C and E.
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Affiliation(s)
- Fengyuan Liu
- School of Food Science and Engineering, South China University of Technology, Guangzhou, 510641, China
| | - Nan Xiang
- School of Food Science and Engineering, South China University of Technology, Guangzhou, 510641, China
| | - Jian Guang Hu
- Crop Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.,Key Laboratory of Crops Genetics Improvement of Guangdong Province, Guangzhou, 510640, China
| | - Yan Shijuan
- Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Lihua Xie
- School of Food Science and Engineering, South China University of Technology, Guangzhou, 510641, China
| | - Charles Stephen Brennan
- School of Food Science and Engineering, South China University of Technology, Guangzhou, 510641, China.,Department of Wine, Food and Molecular Bioscience, Lincoln University, Canterbury, 7647, New Zealand
| | - Wenjie Huang
- Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Xinbo Guo
- School of Food Science and Engineering, South China University of Technology, Guangzhou, 510641, China.
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Hakeem KR, Sabir M, Ozturk M, Akhtar MS, Ibrahim FH. Nitrate and Nitrogen Oxides: Sources, Health Effects and Their Remediation. REVIEWS OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2017; 242:183-217. [PMID: 27734212 DOI: 10.1007/398_2016_11] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Increased use of nitrogenous (N) fertilizers in agriculture has significantly altered the global N-cycle because they release nitrogenous gases of environmental concerns. The emission of nitrous oxide (N2O) contributes to the global greenhouse gas accumulation and the stratospheric ozone depletion. In addition, it causes nitrate leaching problem deteriorating ground water quality. The nitrate toxicity has been reported in a number of studies showing the health hazards like methemoglobinemia in infants and is a potent cause of cancer. Despite these evident negative environmental as well as health impacts, consumption of N fertilizer cannot be reduced in view of the food security for the teeming growing world population. Various agronomic and genetic modifications have been practiced to tackle this problem. Some agronomic techniques adopted include split application of N, use of slow-release fertilizers, nitrification inhibitors and encouraging the use of organic manure over chemical fertilizers. As a matter of fact, the use of chemical means to remediate nitrate from the environment is very difficult and costly. Particularly, removal of nitrate from water is difficult task because it is chemically non-reactive in dilute aqueous solutions. Hence, the use of biological means for nitrate remediation offers a promising strategy to minimize the ill effects of nitrates and nitrites. One of the important goals to reduce N-fertilizer application can be effectively achieved by choosing N-efficient genotypes. This will ensure the optimum uptake of applied N in a balanced manner and exploring the molecular mechanisms for their uptake as well as metabolism in assimilatory pathways. The objectives of this paper are to evaluate the interrelations which exist in the terrestrial ecosystems between the plant type and characteristics of nutrient uptake and analyze the global consumption and demand for fertilizer nitrogen in relation to cereal production, evaluate the various methods used to determine nitrogen use efficincy (NUE), determine NUE for the major cereals grown across large agroclimatic regions, determine the key factors that control NUE, and finally analyze various strategies available to improve the use efficiency of fertilizer nitrogen.
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Affiliation(s)
- Khalid Rehman Hakeem
- Faculty of Forestry, Universiti Putra Malaysia, Serdang, Selangor, UPM 43400, Malaysia.
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia.
| | - Muhammad Sabir
- Institute of Soil and Environmental Sciences, University of Agriculture, Faisalabad, Pakistan
| | - Munir Ozturk
- Botany Department & Centre for Environmental Studies, Ege University, Izmir, Turkey
| | - Mohd Sayeed Akhtar
- Department of Botany, Gandhi Faiz-E-Aam College, Shahjahanpur, 242001, Uttar Pradesh, India
| | - Faridah Hanum Ibrahim
- Faculty of Forestry, Universiti Putra Malaysia, Serdang, Selangor, UPM 43400, Malaysia
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De Haan RL, Schuiteman MA, Vos RJ. Residual soil nitrate content and profitability of five cropping systems in northwest Iowa. PLoS One 2017; 12:e0171994. [PMID: 28248976 PMCID: PMC5332022 DOI: 10.1371/journal.pone.0171994] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 01/30/2017] [Indexed: 11/18/2022] Open
Abstract
Many communities in the Midwestern United States obtain their drinking water from shallow alluvial wells that are vulnerable to contamination by NO3-N from the surrounding agricultural landscape. The objective of this research was to assess cropping systems with the potential to produce a reasonable return for farmers while simultaneously reducing the risk of NO3-N movement into these shallow aquifers. From 2009 to 2013 we conducted a field experiment in northwest Iowa in which we evaluated five cropping systems for residual (late fall) soil NO3-N content and profitability. Soil samples were taken annually from the top 30 cm of the soil profile in June and August, and from the top 180 cm in November (late fall). The November samples were divided into 30 cm increments for analysis. Average residual NO3-N content in the top 180 cm of the soil profile following the 2010 to 2013 cropping years was 134 kg ha-1 for continuous maize (Zea mays L.) with a cereal rye (Secale cereale L.) cover crop, 18 kg ha-1 for perennial grass, 60 kg ha-1 for a three year oat (Avena sativa L.)-alfalfa (Medicago sativa L.)-maize rotation, 85 kg ha-1 for a two year oat/red clover (Trifolium pratense L.)-maize rotation, and 90 kg ha-1 for a three year soybean (Glycine max (L.) Merr.)-winter wheat (Triticum aestivum L.)-maize rotation. However, residual NO3-N in the 90 to 180 cm increment of the soil profile was not significantly higher in the oat-alfalfa-maize cropping system than the perennial grass system. For 2010 to 2013, average profit ($ ha-1 yr-1) was 531 for continuous corn, 347 for soybean-winter wheat-maize, 264 for oat-alfalfa-maize, 140 for oat/red clover-maize, and -384 (loss) for perennial grass. Considering both residual soil NO3-N and profitability data, the oat-alfalfa-maize rotation performed the best in this setting. However, given current economic pressures widespread adoption is likely to require changes in public policy.
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Affiliation(s)
- Robert L. De Haan
- Environmental Studies Department, Dordt College, Sioux Center, Iowa, United States of America
- * E-mail:
| | | | - Ronald J. Vos
- Agriculture Department, Dordt College, Sioux Center, Iowa, United States of America
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30
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Yesbergenova-Cuny Z, Dinant S, Martin-Magniette ML, Quilleré I, Armengaud P, Monfalet P, Lea PJ, Hirel B. Genetic variability of the phloem sap metabolite content of maize (Zea mays L.) during the kernel-filling period. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 252:347-357. [PMID: 27717471 DOI: 10.1016/j.plantsci.2016.08.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 08/08/2016] [Accepted: 08/09/2016] [Indexed: 06/06/2023]
Abstract
Using a metabolomic approach, we have quantified the metabolite composition of the phloem sap exudate of seventeen European and American lines of maize that had been previously classified into five main groups on the basis of molecular marker polymorphisms. In addition to sucrose, glutamate and aspartate, which are abundant in the phloem sap of many plant species, large quantities of aconitate and alanine were also found in the phloem sap exudates of maize. Genetic variability of the phloem sap composition was observed in the different maize lines, although there was no obvious relationship between the phloem sap composition and the five previously classified groups. However, following hierarchical clustering analysis there was a clear relationship between two of the subclusters of lines defined on the basis of the composition of the phloem sap exudate and the earliness of silking date. A comparison between the metabolite contents of the ear leaves and the phloem sap exudates of each genotype, revealed that the relative content of most of the carbon- and nitrogen-containing metabolites was similar. Correlation studies performed between the metabolite content of the phloem sap exudates and yield-related traits also revealed that for some carbohydrates such as arabitol and sucrose there was a negative or positive correlation with kernel yield and kernel weight respectively. A posititive correlation was also found between kernel number and soluble histidine.
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Affiliation(s)
- Zhazira Yesbergenova-Cuny
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, INRA, Centre de Versailles-Grignon, Unité Mixte de Recherche 1318 INRA-Agro-ParisTech, Equipe de Recherce Labellisée (ERL), Centre National de la Recherche Scientifique, CNRS 3559, RD10(,) F-78026 Versailles Cedex, France
| | - Sylvie Dinant
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, INRA, Centre de Versailles-Grignon, Unité Mixte de Recherche 1318 INRA-Agro-ParisTech, Equipe de Recherce Labellisée (ERL), Centre National de la Recherche Scientifique, CNRS 3559, RD10(,) F-78026 Versailles Cedex, France
| | - Marie-Laure Martin-Magniette
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Batiment 630, 91405 Orsay, France; Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405, Orsay, France; UMR MIA-Paris, AgroParisTech, INRA, Université Paris-Saclay, 75005, Paris, France
| | - Isabelle Quilleré
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, INRA, Centre de Versailles-Grignon, Unité Mixte de Recherche 1318 INRA-Agro-ParisTech, Equipe de Recherce Labellisée (ERL), Centre National de la Recherche Scientifique, CNRS 3559, RD10(,) F-78026 Versailles Cedex, France
| | - Patrick Armengaud
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, INRA, Centre de Versailles-Grignon, Unité Mixte de Recherche 1318 INRA-Agro-ParisTech, Equipe de Recherce Labellisée (ERL), Centre National de la Recherche Scientifique, CNRS 3559, RD10(,) F-78026 Versailles Cedex, France
| | - Priscilla Monfalet
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, INRA, Centre de Versailles-Grignon, Unité Mixte de Recherche 1318 INRA-Agro-ParisTech, Equipe de Recherce Labellisée (ERL), Centre National de la Recherche Scientifique, CNRS 3559, RD10(,) F-78026 Versailles Cedex, France; UMR MIA-Paris, AgroParisTech, INRA, Université Paris-Saclay, 75005, Paris, France
| | - Peter J Lea
- Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, United Kingdom
| | - Bertrand Hirel
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, INRA, Centre de Versailles-Grignon, Unité Mixte de Recherche 1318 INRA-Agro-ParisTech, Equipe de Recherce Labellisée (ERL), Centre National de la Recherche Scientifique, CNRS 3559, RD10(,) F-78026 Versailles Cedex, France.
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31
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Beatty PH, Klein MS, Fischer JJ, Lewis IA, Muench DG, Good AG. Understanding Plant Nitrogen Metabolism through Metabolomics and Computational Approaches. PLANTS 2016; 5:plants5040039. [PMID: 27735856 PMCID: PMC5198099 DOI: 10.3390/plants5040039] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 09/21/2016] [Accepted: 09/30/2016] [Indexed: 01/24/2023]
Abstract
A comprehensive understanding of plant metabolism could provide a direct mechanism for improving nitrogen use efficiency (NUE) in crops. One of the major barriers to achieving this outcome is our poor understanding of the complex metabolic networks, physiological factors, and signaling mechanisms that affect NUE in agricultural settings. However, an exciting collection of computational and experimental approaches has begun to elucidate whole-plant nitrogen usage and provides an avenue for connecting nitrogen-related phenotypes to genes. Herein, we describe how metabolomics, computational models of metabolism, and flux balance analysis have been harnessed to advance our understanding of plant nitrogen metabolism. We introduce a model describing the complex flow of nitrogen through crops in a real-world agricultural setting and describe how experimental metabolomics data, such as isotope labeling rates and analyses of nutrient uptake, can be used to refine these models. In summary, the metabolomics/computational approach offers an exciting mechanism for understanding NUE that may ultimately lead to more effective crop management and engineered plants with higher yields.
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Affiliation(s)
- Perrin H Beatty
- Department of Biological Sciences, University of Alberta, 85 Avenue NW, Edmonton, AB T6G 2E9, Canada.
| | - Matthias S Klein
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada.
| | - Jeffrey J Fischer
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada.
| | - Ian A Lewis
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada.
| | - Douglas G Muench
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada.
| | - Allen G Good
- Department of Biological Sciences, University of Alberta, 85 Avenue NW, Edmonton, AB T6G 2E9, Canada.
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32
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Plett D, Holtham L, Baumann U, Kalashyan E, Francis K, Enju A, Toubia J, Roessner U, Bacic A, Rafalski A, Dhugga KS, Tester M, Garnett T, Kaiser BN. Nitrogen assimilation system in maize is regulated by developmental and tissue-specific mechanisms. PLANT MOLECULAR BIOLOGY 2016; 92:293-312. [PMID: 27511191 DOI: 10.1007/s11103-016-0512-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 07/10/2016] [Indexed: 05/21/2023]
Abstract
We found metabolites, enzyme activities and enzyme transcript abundances vary significantly across the maize lifecycle, but weak correlation exists between the three groups. We identified putative genes regulating nitrate assimilation. Progress in improving nitrogen (N) use efficiency (NUE) of crop plants has been hampered by the complexity of the N uptake and utilisation systems. To understand this complexity we measured the activities of seven enzymes and ten metabolites related to N metabolism in the leaf and root tissues of Gaspe Flint maize plants grown in 0.5 or 2.5 mM NO3 (-) throughout the lifecycle. The amino acids had remarkably similar profiles across the lifecycle except for transient responses, which only appeared in the leaves for aspartate or in the roots for asparagine, serine and glycine. The activities of the enzymes for N assimilation were also coordinated to a certain degree, most noticeably with a peak in root activity late in the lifecycle, but with wide variation in the activity levels over the course of development. We analysed the transcriptional data for gene sets encoding the measured enzymes and found that, unlike the enzyme activities, transcript levels of the corresponding genes did not exhibit the same coordination across the lifecycle and were only weakly correlated with the levels of various amino acids or individual enzyme activities. We identified gene sets which were correlated with the enzyme activity profiles, including seven genes located within previously known quantitative trait loci for enzyme activities and hypothesise that these genes are important for the regulation of enzyme activities. This work provides insights into the complexity of the N assimilation system throughout development and identifies candidate regulatory genes, which warrant further investigation in efforts to improve NUE in crop plants.
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Affiliation(s)
- Darren Plett
- Australian Centre for Plant Functional Genomics, Waite Research Institute, University of Adelaide, Adelaide, SA, 5064, Australia
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, SA, 5064, Australia
| | - Luke Holtham
- Australian Centre for Plant Functional Genomics, Waite Research Institute, University of Adelaide, Adelaide, SA, 5064, Australia
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, SA, 5064, Australia
| | - Ute Baumann
- Australian Centre for Plant Functional Genomics, Waite Research Institute, University of Adelaide, Adelaide, SA, 5064, Australia
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, SA, 5064, Australia
| | - Elena Kalashyan
- Australian Centre for Plant Functional Genomics, Waite Research Institute, University of Adelaide, Adelaide, SA, 5064, Australia
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, SA, 5064, Australia
| | - Karen Francis
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, SA, 5064, Australia
| | - Akiko Enju
- Australian Centre for Plant Functional Genomics, Waite Research Institute, University of Adelaide, Adelaide, SA, 5064, Australia
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, SA, 5064, Australia
| | - John Toubia
- Australian Centre for Plant Functional Genomics, Waite Research Institute, University of Adelaide, Adelaide, SA, 5064, Australia
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, SA, 5064, Australia
- ACRF South Australian Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide, SA, 5000, Australia
- School of Molecular and Biomedical Science, The University of Adelaide, Adelaide, SA, 5000, Australia
| | - Ute Roessner
- Australian Centre for Plant Functional Genomics, School of BioSciences, The University of Melbourne, Parkville, VIC, 3010, Australia
- Metabolomics Australia, School of BioSciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Antony Bacic
- Metabolomics Australia, School of BioSciences, The University of Melbourne, Parkville, VIC, 3010, Australia
- ARC Centre of Excellence in Plant Cell Walls, School of BioSciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | | | - Kanwarpal S Dhugga
- DuPont Pioneer, Johnston, IA, 50131, USA
- International Maize and Wheat Improvement Center (CIMMYT), Carretera México Veracruz, Km. 45, El Batán, Texcoco, Estado De México, 56237, USA
| | - Mark Tester
- Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Trevor Garnett
- Australian Centre for Plant Functional Genomics, Waite Research Institute, University of Adelaide, Adelaide, SA, 5064, Australia.
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, SA, 5064, Australia.
- The Plant Accelerator, Australian Plant Phenomics Facility, The University of Adelaide, PMB 1, Glen Osmond, 5064, Australia.
| | - Brent N Kaiser
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, SA, 5064, Australia
- Centre For Carbon Water and Food, The Faculty of Agriculture and Environment, The University of Sydney, Camden, NSW, 2570, Australia
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Batista Silva W, Daloso DM, Fernie AR, Nunes-Nesi A, Araújo WL. Can stable isotope mass spectrometry replace radiolabelled approaches in metabolic studies? PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 249:59-69. [PMID: 27297990 DOI: 10.1016/j.plantsci.2016.05.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 04/21/2016] [Accepted: 05/13/2016] [Indexed: 05/03/2023]
Abstract
Metabolic pathways and the key regulatory points thereof can be deduced using isotopically labelled substrates. One prerequisite is the accurate measurement of the labeling pattern of targeted metabolites. The subsequent estimation of metabolic fluxes following incubation in radiolabelled substrates has been extensively used. Radiolabelling is a sensitive approach and allows determination of total label uptake since the total radiolabel content is easy to detect. However, the incubation of cells, tissues or the whole plant in a stable isotope enriched environment and the use of either mass spectrometry or nuclear magnetic resonance techniques to determine label incorporation within specific metabolites offers the possibility to readily obtain metabolic information with higher resolution. It additionally also offers an important complement to other post-genomic strategies such as metabolite profiling providing insights into the regulation of the metabolic network and thus allowing a more thorough description of plant cellular function. Thus, although safety concerns mean that stable isotope feeding is generally preferred, the techniques are in truth highly complementary and application of both approaches in tandem currently probably provides the best route towards a comprehensive understanding of plant cellular metabolism.
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Affiliation(s)
- Willian Batista Silva
- Max Planck Partner Group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa-MG, Brazil.
| | - Danilo M Daloso
- Max-Planck-Institute of Molecular Plant Physiology Am Mühlenberg 1, 14476,Golm Potsdam, Germany.
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology Am Mühlenberg 1, 14476,Golm Potsdam, Germany.
| | - Adriano Nunes-Nesi
- Max Planck Partner Group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa-MG, Brazil.
| | - Wagner L Araújo
- Max Planck Partner Group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa-MG, Brazil.
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Sun C, Li Y, Zhao W, Song X, Lu M, Li X, Li X, Liu R, Yan L, Zhang X. Integration of Hormonal and Nutritional Cues Orchestrates Progressive Corolla Opening. PLANT PHYSIOLOGY 2016; 171:1209-29. [PMID: 27208289 PMCID: PMC4902604 DOI: 10.1104/pp.16.00209] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 04/24/2016] [Indexed: 05/19/2023]
Abstract
Flower opening is essential for pollination and thus successful sexual reproduction; however, the underlying mechanisms of its timing control remain largely elusive. We identify a unique cucumber (Cucumis sativus) line '6457' that produces normal ovaries when nutrients are under-supplied, and super ovaries (87%) with delayed corolla opening when nutrients are oversupplied. Corolla opening in both normal and super ovaries is divided into four distinct phases, namely the green bud, green-yellow bud, yellow bud, and flowering stages, along with progressive color transition, cytological tuning, and differential expression of 14,282 genes. In the super ovary, cell division and cell expansion persisted for a significantly longer period of time; the expressions of genes related to photosynthesis, protein degradation, and signaling kinases were dramatically up-regulated, whereas the activities of most transcription factors and stress-related genes were significantly down-regulated; concentrations of cytokinins (CKs) and gibberellins were higher in accordance with reduced cytokinin conjugation and degradation and increased expression of gibberellin biosynthesis genes. Exogenous CK application was sufficient for the genesis of super ovaries, suggesting a decisive role of CKs in controlling the timing of corolla opening. Furthermore, 194 out of 11,127 differentially expressed genes identified in pairwise comparisons, including critical developmental, signaling, and cytological regulators, contained all three types of cis-elements for CK, nitrate, and phosphorus responses in their promoter regions, indicating that the integration of hormone modulation and nutritional regulation orchestrated the precise control of corolla opening in cucumber. Our findings provide a valuable framework for dissecting the regulatory pathways for flower opening in plants.
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Affiliation(s)
- Chengzhen Sun
- College of Horticulture Science and Technology (C.S., M.L., Xi.L., L.Y.) and Analysis and Testing Centre (X.S.), Hebei Normal University of Science and Technology, Qinhuangdao 066004, China;Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201602, China (Y.L., R.L.);Department of Vegetable Sciences, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China (W.Z., X.Z.); andDepartment of Plant Nutrition, Key Laboratory of Plant-Soil Interactions, China Agricultural University, Beijing 100193, China (Xu.L.)
| | - Yanqiang Li
- College of Horticulture Science and Technology (C.S., M.L., Xi.L., L.Y.) and Analysis and Testing Centre (X.S.), Hebei Normal University of Science and Technology, Qinhuangdao 066004, China;Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201602, China (Y.L., R.L.);Department of Vegetable Sciences, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China (W.Z., X.Z.); andDepartment of Plant Nutrition, Key Laboratory of Plant-Soil Interactions, China Agricultural University, Beijing 100193, China (Xu.L.)
| | - Wensheng Zhao
- College of Horticulture Science and Technology (C.S., M.L., Xi.L., L.Y.) and Analysis and Testing Centre (X.S.), Hebei Normal University of Science and Technology, Qinhuangdao 066004, China;Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201602, China (Y.L., R.L.);Department of Vegetable Sciences, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China (W.Z., X.Z.); andDepartment of Plant Nutrition, Key Laboratory of Plant-Soil Interactions, China Agricultural University, Beijing 100193, China (Xu.L.)
| | - Xiaofei Song
- College of Horticulture Science and Technology (C.S., M.L., Xi.L., L.Y.) and Analysis and Testing Centre (X.S.), Hebei Normal University of Science and Technology, Qinhuangdao 066004, China;Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201602, China (Y.L., R.L.);Department of Vegetable Sciences, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China (W.Z., X.Z.); andDepartment of Plant Nutrition, Key Laboratory of Plant-Soil Interactions, China Agricultural University, Beijing 100193, China (Xu.L.)
| | - Man Lu
- College of Horticulture Science and Technology (C.S., M.L., Xi.L., L.Y.) and Analysis and Testing Centre (X.S.), Hebei Normal University of Science and Technology, Qinhuangdao 066004, China;Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201602, China (Y.L., R.L.);Department of Vegetable Sciences, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China (W.Z., X.Z.); andDepartment of Plant Nutrition, Key Laboratory of Plant-Soil Interactions, China Agricultural University, Beijing 100193, China (Xu.L.)
| | - Xiaoli Li
- College of Horticulture Science and Technology (C.S., M.L., Xi.L., L.Y.) and Analysis and Testing Centre (X.S.), Hebei Normal University of Science and Technology, Qinhuangdao 066004, China;Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201602, China (Y.L., R.L.);Department of Vegetable Sciences, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China (W.Z., X.Z.); andDepartment of Plant Nutrition, Key Laboratory of Plant-Soil Interactions, China Agricultural University, Beijing 100193, China (Xu.L.)
| | - Xuexian Li
- College of Horticulture Science and Technology (C.S., M.L., Xi.L., L.Y.) and Analysis and Testing Centre (X.S.), Hebei Normal University of Science and Technology, Qinhuangdao 066004, China;Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201602, China (Y.L., R.L.);Department of Vegetable Sciences, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China (W.Z., X.Z.); andDepartment of Plant Nutrition, Key Laboratory of Plant-Soil Interactions, China Agricultural University, Beijing 100193, China (Xu.L.)
| | - Renyi Liu
- College of Horticulture Science and Technology (C.S., M.L., Xi.L., L.Y.) and Analysis and Testing Centre (X.S.), Hebei Normal University of Science and Technology, Qinhuangdao 066004, China;Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201602, China (Y.L., R.L.);Department of Vegetable Sciences, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China (W.Z., X.Z.); andDepartment of Plant Nutrition, Key Laboratory of Plant-Soil Interactions, China Agricultural University, Beijing 100193, China (Xu.L.)
| | - Liying Yan
- College of Horticulture Science and Technology (C.S., M.L., Xi.L., L.Y.) and Analysis and Testing Centre (X.S.), Hebei Normal University of Science and Technology, Qinhuangdao 066004, China;Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201602, China (Y.L., R.L.);Department of Vegetable Sciences, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China (W.Z., X.Z.); andDepartment of Plant Nutrition, Key Laboratory of Plant-Soil Interactions, China Agricultural University, Beijing 100193, China (Xu.L.)
| | - Xiaolan Zhang
- College of Horticulture Science and Technology (C.S., M.L., Xi.L., L.Y.) and Analysis and Testing Centre (X.S.), Hebei Normal University of Science and Technology, Qinhuangdao 066004, China;Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201602, China (Y.L., R.L.);Department of Vegetable Sciences, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China (W.Z., X.Z.); andDepartment of Plant Nutrition, Key Laboratory of Plant-Soil Interactions, China Agricultural University, Beijing 100193, China (Xu.L.)
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Lv Y, Liang Z, Ge M, Qi W, Zhang T, Lin F, Peng Z, Zhao H. Genome-wide identification and functional prediction of nitrogen-responsive intergenic and intronic long non-coding RNAs in maize (Zea mays L.). BMC Genomics 2016; 17:350. [PMID: 27169379 PMCID: PMC4865003 DOI: 10.1186/s12864-016-2650-1] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 04/23/2016] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Nitrogen (N) is an essential and often limiting nutrient to plant growth and development. Previous studies have shown that the mRNA expressions of numerous genes are regulated by nitrogen supplies; however, little is known about the expressed non-coding elements, for example long non-coding RNAs (lncRNAs) that control the response of maize (Zea mays L.) to nitrogen. LncRNAs are a class of non-coding RNAs larger than 200 bp, which have emerged as key regulators in gene expression. RESULTS In this study, we surveyed the intergenic/intronic lncRNAs in maize B73 leaves at the V7 stage under conditions of N-deficiency and N-sufficiency using ribosomal RNA depletion and ultra-deep total RNA sequencing approaches. By integration with mRNA expression profiles and physiological evaluations, 7245 lncRNAs and 637 nitrogen-responsive lncRNAs were identified that exhibited unique expression patterns. Co-expression network analysis showed that the nitrogen-responsive lncRNAs were enriched mainly in one of the three co-expressed modules. The genes in the enriched module are mainly involved in NADH dehydrogenase activity, oxidative phosphorylation and the nitrogen compounds metabolic process. CONCLUSIONS We identified a large number of lncRNAs in maize and illustrated their potential regulatory roles in response to N stress. The results lay the foundation for further in-depth understanding of the molecular mechanisms of lncRNAs' role in response to nitrogen stresses.
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Affiliation(s)
- Yuanda Lv
- Provincial Key Laboratory of Agrobiology, Institute of Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, China.,Department of Biochemistry and Molecular Biology, Mississippi State University, Mississippi, Mississippi State, USA
| | - Zhikai Liang
- Department of Biochemistry and Molecular Biology, Mississippi State University, Mississippi, Mississippi State, USA
| | - Min Ge
- Provincial Key Laboratory of Agrobiology, Institute of Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Weicong Qi
- Provincial Key Laboratory of Agrobiology, Institute of Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Tifu Zhang
- Provincial Key Laboratory of Agrobiology, Institute of Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Feng Lin
- Provincial Key Laboratory of Agrobiology, Institute of Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Zhaohua Peng
- Department of Biochemistry and Molecular Biology, Mississippi State University, Mississippi, Mississippi State, USA.
| | - Han Zhao
- Provincial Key Laboratory of Agrobiology, Institute of Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, China.
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Plett D, Baumann U, Schreiber AW, Holtham L, Kalashyan E, Toubia J, Nau J, Beatty M, Rafalski A, Dhugga KS, Tester M, Garnett T, Kaiser BN. Maize maintains growth in response to decreased nitrate supply through a highly dynamic and developmental stage-specific transcriptional response. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:342-53. [PMID: 26038196 DOI: 10.1111/pbi.12388] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 03/18/2015] [Accepted: 03/24/2015] [Indexed: 05/10/2023]
Abstract
Elucidation of the gene networks underlying the response to N supply and demand will facilitate the improvement of the N uptake efficiency of plants. We undertook a transcriptomic analysis of maize to identify genes responding to both a non-growth-limiting decrease in NO3- provision and to development-based N demand changes at seven representative points across the life cycle. Gene co-expression networks were derived by cluster analysis of the transcript profiles. The majority of NO3--responsive transcription occurred at 11 (D11), 18 (D18) and 29 (D29) days after emergence, with differential expression predominating in the root at D11 and D29 and in the leaf at D18. A cluster of 98 probe sets was identified, the expression pattern of which is similar to that of the high-affinity NO3- transporter (NRT2) genes across the life cycle. The cluster is enriched with genes encoding enzymes and proteins of lipid metabolism and transport, respectively. These are candidate genes for the response of maize to N supply and demand. Only a few patterns of differential gene expression were observed over the entire life cycle; however, the composition of the classes of the genes differentially regulated at individual time points was unique, suggesting tightly controlled regulation of NO3--responsive gene expression.
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Affiliation(s)
- Darren Plett
- Australian Centre for Plant Functional Genomics, Waite Research Institute, University of Adelaide, Adelaide, SA, Australia
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, SA, Australia
| | - Ute Baumann
- Australian Centre for Plant Functional Genomics, Waite Research Institute, University of Adelaide, Adelaide, SA, Australia
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, SA, Australia
| | - Andreas W Schreiber
- Australian Centre for Plant Functional Genomics, Waite Research Institute, University of Adelaide, Adelaide, SA, Australia
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, SA, Australia
| | - Luke Holtham
- Australian Centre for Plant Functional Genomics, Waite Research Institute, University of Adelaide, Adelaide, SA, Australia
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, SA, Australia
| | - Elena Kalashyan
- Australian Centre for Plant Functional Genomics, Waite Research Institute, University of Adelaide, Adelaide, SA, Australia
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, SA, Australia
| | - John Toubia
- Australian Centre for Plant Functional Genomics, Waite Research Institute, University of Adelaide, Adelaide, SA, Australia
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, SA, Australia
| | - John Nau
- DuPont Pioneer, Johnston, IA, USA
| | | | | | | | - Mark Tester
- Division of Biological and Environmental Sciences and Engineering, 4700 King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Trevor Garnett
- Australian Centre for Plant Functional Genomics, Waite Research Institute, University of Adelaide, Adelaide, SA, Australia
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, SA, Australia
| | - Brent N Kaiser
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, SA, Australia
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37
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Chen Q, Liu Z, Wang B, Wang X, Lai J, Tian F. Transcriptome sequencing reveals the roles of transcription factors in modulating genotype by nitrogen interaction in maize. PLANT CELL REPORTS 2015; 34:1761-71. [PMID: 26116219 PMCID: PMC4569664 DOI: 10.1007/s00299-015-1822-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Revised: 06/06/2015] [Accepted: 06/10/2015] [Indexed: 05/07/2023]
Abstract
Global transcriptome analysis in maize revealed differential nitrogen response between genotypes and implicate a crucial role of transcription factors in driving genotype by nitrogen interactions at gene expression level. Developing nitrogen-efficient cultivars are essential for sustainable and productive agriculture. Nitrogen use efficiency of plants is highly dependent on the interaction of environmental and genetic variation and results in adaptive phenotypes. This study used transcriptome sequencing to perform a comprehensive genotype by nitrogen (G × N) interaction analysis for two elite Chinese maize inbreds grown at normal and low nitrogen levels in field conditions. We demonstrated that the two maize inbreds showed contrasting agronomic and transcriptomic responses to changes in nitrogen availability. A total of 96 genes with a significant G × N interaction were detected. After characterizing the expression patterns of G × N interaction genes, we found that the G × N interaction genes tended to show condition-specific differential expression. The functional annotations of G × N interaction genes revealed that many different kinds of genes were involved in G × N interactions, but a significant enrichment for transcription factors was detected, particularly the AP2/EREBP and WRKY family, suggesting that transcription factors might play important roles in driving G × N interaction at gene expression level for nitrogen response in maize. Taken together, these results not only provide novel insights into the mechanism of nitrogen response in maize and set important basis for further characterization but also have important implications for other genotype by stress interaction.
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Affiliation(s)
- Qiuyue Chen
- National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
| | - Zhipeng Liu
- National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
| | - Baobao Wang
- National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
| | - Xufeng Wang
- National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
| | - Jinsheng Lai
- National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
| | - Feng Tian
- National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China.
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38
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Dash M, Yordanov YS, Georgieva T, Kumari S, Wei H, Busov V. A systems biology approach identifies new regulators of poplar root development under low nitrogen. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 84:335-46. [PMID: 26315649 DOI: 10.1111/tpj.13002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 08/14/2015] [Accepted: 08/20/2015] [Indexed: 05/02/2023]
Abstract
In Populus, low nitrogen (LN) elicits rapid and vigorous lateral root (LR) proliferation, which is closely mirrored by corresponding transcriptomic changes. Using transcriptomic data, we built a genetic network encompassing a large proportion of the differentially regulated transcriptome. The network is organized in a hierarchical fashion, centered on 11 genes. Transgenic manipulations of only three of the 11 genes had a strong impact on root development under LN. These three genes encoded an F-box protein similar to Hawaiian Skirt (PtaHWS) and two transcription factors (PtaRAP2.11 and PtaNAC1). Up- and downregulation of the three genes caused increased and decreased root proliferation under LN conditions, respectively. The transgenic manipulations had a strong positive effect on growth under greenhouse conditions including increased shoot and root biomass. The three genes appeared to encompass a putative yet-unknown mechanism that underlies root development under LN. Specifically, the genes are predominantly expressed in roots and have a similar temporal response to LN. More importantly, transgenic manipulation for each of the three genes had a highly significant impact on the expression of the other two. The transgenic manipulations appear to also affect the expression of the regulatory miRNA (PtamiRNA164e) of one of the transcription factors (PtaNAC1), albeit in an opposite fashion. Consistent with a putative function of PtaHWS in proteasome degradation, treatment with proteasome inhibitor reversed the expression changes in the transgenic plants. The insights from this study will allow genetic modifications of root architecture for more efficient and dynamic nitrogen foraging in biofuel crops like poplar.
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Affiliation(s)
- Madhumita Dash
- Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931, USA
| | - Yordan S Yordanov
- Department of Biological Sciences, Eastern Illinois University, Charleston, IL, 61920, USA
| | - Tatyana Georgieva
- Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931, USA
| | - Sapna Kumari
- Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931, USA
| | - Hairong Wei
- Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931, USA
| | - Victor Busov
- Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931, USA
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Gong F, Yang L, Tai F, Hu X, Wang W. "Omics" of maize stress response for sustainable food production: opportunities and challenges. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2015; 18:714-32. [PMID: 25401749 DOI: 10.1089/omi.2014.0125] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Maize originated in the highlands of Mexico approximately 8700 years ago and is one of the most commonly grown cereal crops worldwide, followed by wheat and rice. Abiotic stresses (primarily drought, salinity, and high and low temperatures), together with biotic stresses (primarily fungi, viruses, and pests), negatively affect maize growth, development, and eventually production. To understand the response of maize to abiotic and biotic stresses and its mechanism of stress tolerance, high-throughput omics approaches have been used in maize stress studies. Integrated omics approaches are crucial for dissecting the temporal and spatial system-level changes that occur in maize under various stresses. In this comprehensive analysis, we review the primary types of stresses that threaten sustainable maize production; underscore the recent advances in maize stress omics, especially proteomics; and discuss the opportunities, challenges, and future directions of maize stress omics, with a view to sustainable food production. The knowledge gained from studying maize stress omics is instrumental for improving maize to cope with various stresses and to meet the food demands of the exponentially growing global population. Omics systems science offers actionable potential solutions for sustainable food production, and we present maize as a notable case study.
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Affiliation(s)
- Fangping Gong
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Science, Henan Agricultural University , Zhengzhou, China
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40
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Medeiros DB, Daloso DM, Fernie AR, Nikoloski Z, Araújo WL. Utilizing systems biology to unravel stomatal function and the hierarchies underpinning its control. PLANT, CELL & ENVIRONMENT 2015; 38:1457-70. [PMID: 25689387 DOI: 10.1111/pce.12517] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2014] [Revised: 01/20/2015] [Accepted: 01/27/2015] [Indexed: 05/08/2023]
Abstract
Stomata control the concomitant exchange of CO2 and transpiration in land plants. While a constant supply of CO2 is need to maintain the rate of photosynthesis, the accompanying water losses must be tightly regulated to prevent dehydration and undesired metabolic changes. The factors affecting stomatal movement are directly coupled with the cellular networks of guard cells. Although the guard cell has been used as a model for characterization of signaling pathways, several important questions about its functioning remain elusive. Current modeling approaches describe the stomatal conductance in terms of relatively few easy-to-measure variables being unsuitable for in silico design of genetic manipulation strategies. Here, we argue that a system biology approach, combining modeling and high-throughput experiments, may be used to elucidate the mechanisms underlying stomata control and to determine targets for modulation of stomatal responses to environment. In support of our opinion, we review studies demonstrating how high-throughput approaches have provided a systems-view of guard cells. Finally, we emphasize the opportunities and challenges of genome-scale modeling and large-scale data integration for in silico manipulation of guard cell functions to improve crop yields, particularly under stress conditions which are of pertinence both to climate change and water use efficiency.
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Affiliation(s)
- David B Medeiros
- Max-Planck Partner Group, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Danilo M Daloso
- Central Metabolism Group, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Alisdair R Fernie
- Central Metabolism Group, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Zoran Nikoloski
- Systems Biology and Mathematical Modeling Group, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Wagner L Araújo
- Max-Planck Partner Group, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
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41
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Technow F, Messina CD, Totir LR, Cooper M. Integrating Crop Growth Models with Whole Genome Prediction through Approximate Bayesian Computation. PLoS One 2015; 10:e0130855. [PMID: 26121133 PMCID: PMC4488317 DOI: 10.1371/journal.pone.0130855] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 05/25/2015] [Indexed: 11/18/2022] Open
Abstract
Genomic selection, enabled by whole genome prediction (WGP) methods, is revolutionizing plant breeding. Existing WGP methods have been shown to deliver accurate predictions in the most common settings, such as prediction of across environment performance for traits with additive gene effects. However, prediction of traits with non-additive gene effects and prediction of genotype by environment interaction (G×E), continues to be challenging. Previous attempts to increase prediction accuracy for these particularly difficult tasks employed prediction methods that are purely statistical in nature. Augmenting the statistical methods with biological knowledge has been largely overlooked thus far. Crop growth models (CGMs) attempt to represent the impact of functional relationships between plant physiology and the environment in the formation of yield and similar output traits of interest. Thus, they can explain the impact of G×E and certain types of non-additive gene effects on the expressed phenotype. Approximate Bayesian computation (ABC), a novel and powerful computational procedure, allows the incorporation of CGMs directly into the estimation of whole genome marker effects in WGP. Here we provide a proof of concept study for this novel approach and demonstrate its use with synthetic data sets. We show that this novel approach can be considerably more accurate than the benchmark WGP method GBLUP in predicting performance in environments represented in the estimation set as well as in previously unobserved environments for traits determined by non-additive gene effects. We conclude that this proof of concept demonstrates that using ABC for incorporating biological knowledge in the form of CGMs into WGP is a very promising and novel approach to improving prediction accuracy for some of the most challenging scenarios in plant breeding and applied genetics.
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Affiliation(s)
- Frank Technow
- Breeding Technologies, DuPont Pioneer, Johnston, IA, USA
- * E-mail:
| | - Carlos D. Messina
- Trait Characterization & Development, DuPont Pioneer, Johnston, IA, USA
| | - L. Radu Totir
- Breeding Technologies, DuPont Pioneer, Johnston, IA, USA
| | - Mark Cooper
- Trait Characterization & Development, DuPont Pioneer, Johnston, IA, USA
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42
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Comadira G, Rasool B, Karpinska B, Morris J, Verrall SR, Hedley PE, Foyer CH, Hancock RD. Nitrogen deficiency in barley (Hordeum vulgare) seedlings induces molecular and metabolic adjustments that trigger aphid resistance. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:3639-55. [PMID: 26038307 PMCID: PMC4463806 DOI: 10.1093/jxb/erv276] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Agricultural nitrous oxide (N2O) pollution resulting from the use of synthetic fertilizers represents a significant contribution to anthropogenic greenhouse gas emissions, providing a rationale for reduced use of nitrogen (N) fertilizers. Nitrogen limitation results in extensive systems rebalancing that remodels metabolism and defence processes. To analyse the regulation underpinning these responses, barley (Horedeum vulgare) seedlings were grown for 7 d under N-deficient conditions until net photosynthesis was 50% lower than in N-replete controls. Although shoot growth was decreased there was no evidence for the induction of oxidative stress despite lower total concentrations of N-containing antioxidants. Nitrogen-deficient barley leaves were rich in amino acids, sugars and tricarboxylic acid cycle intermediates. In contrast to N-replete leaves one-day-old nymphs of the green peach aphid (Myzus persicae) failed to reach adulthood when transferred to N-deficient barley leaves. Transcripts encoding cell, sugar and nutrient signalling, protein degradation and secondary metabolism were over-represented in N-deficient leaves while those associated with hormone metabolism were similar under both nutrient regimes with the exception of mRNAs encoding proteins involved in auxin metabolism and responses. Significant similarities were observed between the N-limited barley leaf transcriptome and that of aphid-infested Arabidopsis leaves. These findings not only highlight significant similarities between biotic and abiotic stress signalling cascades but also identify potential targets for increasing aphid resistance with implications for the development of sustainable agriculture.
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Affiliation(s)
- Gloria Comadira
- Centre for Plant Sciences, Faculty of Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Brwa Rasool
- Centre for Plant Sciences, Faculty of Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Barbara Karpinska
- Centre for Plant Sciences, Faculty of Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Jenny Morris
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | | | - Peter E Hedley
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Christine H Foyer
- Centre for Plant Sciences, Faculty of Biology, University of Leeds, Leeds LS2 9JT, UK
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Gong F, Wu X, Zhang H, Chen Y, Wang W. Making better maize plants for sustainable grain production in a changing climate. FRONTIERS IN PLANT SCIENCE 2015; 6:835. [PMID: 26500671 PMCID: PMC4593952 DOI: 10.3389/fpls.2015.00835] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 09/23/2015] [Indexed: 05/20/2023]
Abstract
Achieving grain supply security with limited arable land is a major challenge in the twenty-first century, owing to the changing climate and increasing global population. Maize plays an increasingly vital role in global grain production. As a C4 plant, maize has a high yield potential. Maize is predicted to become the number one cereal in the world by 2020. However, maize production has plateaued in many countries, and hybrid and production technologies have been fully exploited. Thus, there is an urgent need to shape maize traits and architectures for increased stress tolerance and higher yield in a changing climate. Recent achievements in genomics, proteomics, and metabolomics have provided an unprecedented opportunity to make better maize. In this paper, we discuss the current challenges and potential of maize production, particularly in China. We also highlight the need for enhancing maize tolerance to drought and heat waves, summarize the elite shoot and root traits and phenotypes, and propose an ideotype for sustainable maize production in a changing climate. This will facilitate targeted maize improvement through a conventional breeding program combined with molecular techniques.
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Affiliation(s)
| | | | | | | | - Wei Wang
- *Correspondence: Wei Wang, State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Life Science, Henan Agricultural University, 95 Wenhua Road, Zhengzhou 450002, China,
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Zanin L, Zamboni A, Monte R, Tomasi N, Varanini Z, Cesco S, Pinton R. Transcriptomic Analysis Highlights Reciprocal Interactions of Urea and Nitrate for Nitrogen Acquisition by Maize Roots. ACTA ACUST UNITED AC 2014; 56:532-48. [DOI: 10.1093/pcp/pcu202] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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Amiour N, Imbaud S, Clément G, Agier N, Zivy M, Valot B, Balliau T, Quilleré I, Tercé-Laforgue T, Dargel-Graffin C, Hirel B. An integrated "omics" approach to the characterization of maize (Zea mays L.) mutants deficient in the expression of two genes encoding cytosolic glutamine synthetase. BMC Genomics 2014; 15:1005. [PMID: 25410248 PMCID: PMC4247748 DOI: 10.1186/1471-2164-15-1005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 11/04/2014] [Indexed: 11/21/2022] Open
Abstract
Background To identify the key elements controlling grain production in maize, it is essential to have an integrated view of the responses to alterations in the main steps of nitrogen assimilation by modification of gene expression. Two maize mutant lines (gln1.3 and gln1.4), deficient in two genes encoding cytosolic glutamine synthetase, a key enzyme involved in nitrogen assimilation, were previously characterized by a reduction of kernel size in the gln1.4 mutant and by a reduction of kernel number in the gln1.3 mutant. In this work, the differences in leaf gene transcripts, proteins and metabolite accumulation in gln1.3 and gln1.4 mutants were studied at two key stages of plant development, in order to identify putative candidate genes, proteins and metabolic pathways contributing on one hand to the control of plant development and on the other to grain production. Results The most interesting finding in this study is that a number of key plant processes were altered in the gln1.3 and gln1.4 mutants, including a number of major biological processes such as carbon metabolism and transport, cell wall metabolism, and several metabolic pathways and stress responsive and regulatory elements. We also found that the two mutants share common or specific characteristics across at least two or even three of the “omics” considered at the vegetative stage of plant development, or during the grain filling period. Conclusions This is the first comprehensive molecular and physiological characterization of two cytosolic glutamine synthetase maize mutants using a combined transcriptomic, proteomic and metabolomic approach. We find that the integration of the three “omics” procedures is not straight forward, since developmental and mutant-specific levels of regulation seem to occur from gene expression to metabolite accumulation. However, their potential use is discussed with a view to improving our understanding of nitrogen assimilation and partitioning and its impact on grain production. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1005) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Bertrand Hirel
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique (INRA), Centre de Versailles-Grignon, Unité Mixte de Recherche 1318 INRA-Agro-ParisTech, Equipe de Recherche Labellisée, Centre National de la Recherche Scientifique 3559, RD10, F-78026 Versailles, Cedex, France.
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Calderwood A, Morris RJ, Kopriva S. Predictive sulfur metabolism - a field in flux. FRONTIERS IN PLANT SCIENCE 2014; 5:646. [PMID: 25477892 PMCID: PMC4235266 DOI: 10.3389/fpls.2014.00646] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 11/02/2014] [Indexed: 05/08/2023]
Abstract
The key role of sulfur metabolites in response to biotic and abiotic stress in plants, as well as their importance in diet and health has led to a significant interest and effort in trying to understand and manipulate the production of relevant compounds. Metabolic engineering utilizes a set of theoretical tools to help rationally design modifications that enhance the production of a desired metabolite. Such approaches have proven their value in bacterial systems, however, the paucity of success stories to date in plants, suggests that challenges remain. Here, we review the most commonly used methods for understanding metabolic flux, focusing on the sulfur assimilatory pathway. We highlight known issues with both experimental and theoretical approaches, as well as presenting recent methods for integrating different modeling strategies, and progress toward an understanding of flux at the whole plant level.
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Affiliation(s)
| | - Richard J. Morris
- Department of Computational and Systems Biology, John Innes CentreNorwich, UK
| | - Stanislav Kopriva
- Botanical Institute and Cluster of Excellence on Plant Sciences, University of Cologne, Cologne BiocenterCologne, Germany
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Simons M, Saha R, Amiour N, Kumar A, Guillard L, Clément G, Miquel M, Li Z, Mouille G, Lea PJ, Hirel B, Maranas CD. Assessing the metabolic impact of nitrogen availability using a compartmentalized maize leaf genome-scale model. PLANT PHYSIOLOGY 2014; 166:1659-74. [PMID: 25248718 PMCID: PMC4226342 DOI: 10.1104/pp.114.245787] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Maize (Zea mays) is an important C4 plant due to its widespread use as a cereal and energy crop. A second-generation genome-scale metabolic model for the maize leaf was created to capture C4 carbon fixation and investigate nitrogen (N) assimilation by modeling the interactions between the bundle sheath and mesophyll cells. The model contains gene-protein-reaction relationships, elemental and charge-balanced reactions, and incorporates experimental evidence pertaining to the biomass composition, compartmentalization, and flux constraints. Condition-specific biomass descriptions were introduced that account for amino acids, fatty acids, soluble sugars, proteins, chlorophyll, lignocellulose, and nucleic acids as experimentally measured biomass constituents. Compartmentalization of the model is based on proteomic/transcriptomic data and literature evidence. With the incorporation of information from the MetaCrop and MaizeCyc databases, this updated model spans 5,824 genes, 8,525 reactions, and 9,153 metabolites, an increase of approximately 4 times the size of the earlier iRS1563 model. Transcriptomic and proteomic data have also been used to introduce regulatory constraints in the model to simulate an N-limited condition and mutants deficient in glutamine synthetase, gln1-3 and gln1-4. Model-predicted results achieved 90% accuracy when comparing the wild type grown under an N-complete condition with the wild type grown under an N-deficient condition.
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Affiliation(s)
- Margaret Simons
- Departments of Chemical Engineering (M.S., R.S., C.D.M.) and Bioinformatics and Genomics, Huck Institutes of the Life Sciences (A.K.), Pennsylvania State University, University Park, Pennsylvania 16802;Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, Centre de Versailles-Grignon, Unité Mixte de Recherche 1318 Institut National de la Recherche Agronomique-Agro-ParisTech, Equipe de Recherce Labellisée, Centre National de la Recherche Scientifique 3559, F-78026 Versailles cedex, France (N.A., L.G., G.C., M.M., Z.L., G.M., B.H.); andLancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, United Kingdom (P.J.L.)
| | - Rajib Saha
- Departments of Chemical Engineering (M.S., R.S., C.D.M.) and Bioinformatics and Genomics, Huck Institutes of the Life Sciences (A.K.), Pennsylvania State University, University Park, Pennsylvania 16802;Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, Centre de Versailles-Grignon, Unité Mixte de Recherche 1318 Institut National de la Recherche Agronomique-Agro-ParisTech, Equipe de Recherce Labellisée, Centre National de la Recherche Scientifique 3559, F-78026 Versailles cedex, France (N.A., L.G., G.C., M.M., Z.L., G.M., B.H.); andLancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, United Kingdom (P.J.L.)
| | - Nardjis Amiour
- Departments of Chemical Engineering (M.S., R.S., C.D.M.) and Bioinformatics and Genomics, Huck Institutes of the Life Sciences (A.K.), Pennsylvania State University, University Park, Pennsylvania 16802;Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, Centre de Versailles-Grignon, Unité Mixte de Recherche 1318 Institut National de la Recherche Agronomique-Agro-ParisTech, Equipe de Recherce Labellisée, Centre National de la Recherche Scientifique 3559, F-78026 Versailles cedex, France (N.A., L.G., G.C., M.M., Z.L., G.M., B.H.); andLancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, United Kingdom (P.J.L.)
| | - Akhil Kumar
- Departments of Chemical Engineering (M.S., R.S., C.D.M.) and Bioinformatics and Genomics, Huck Institutes of the Life Sciences (A.K.), Pennsylvania State University, University Park, Pennsylvania 16802;Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, Centre de Versailles-Grignon, Unité Mixte de Recherche 1318 Institut National de la Recherche Agronomique-Agro-ParisTech, Equipe de Recherce Labellisée, Centre National de la Recherche Scientifique 3559, F-78026 Versailles cedex, France (N.A., L.G., G.C., M.M., Z.L., G.M., B.H.); andLancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, United Kingdom (P.J.L.)
| | - Lenaïg Guillard
- Departments of Chemical Engineering (M.S., R.S., C.D.M.) and Bioinformatics and Genomics, Huck Institutes of the Life Sciences (A.K.), Pennsylvania State University, University Park, Pennsylvania 16802;Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, Centre de Versailles-Grignon, Unité Mixte de Recherche 1318 Institut National de la Recherche Agronomique-Agro-ParisTech, Equipe de Recherce Labellisée, Centre National de la Recherche Scientifique 3559, F-78026 Versailles cedex, France (N.A., L.G., G.C., M.M., Z.L., G.M., B.H.); andLancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, United Kingdom (P.J.L.)
| | - Gilles Clément
- Departments of Chemical Engineering (M.S., R.S., C.D.M.) and Bioinformatics and Genomics, Huck Institutes of the Life Sciences (A.K.), Pennsylvania State University, University Park, Pennsylvania 16802;Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, Centre de Versailles-Grignon, Unité Mixte de Recherche 1318 Institut National de la Recherche Agronomique-Agro-ParisTech, Equipe de Recherce Labellisée, Centre National de la Recherche Scientifique 3559, F-78026 Versailles cedex, France (N.A., L.G., G.C., M.M., Z.L., G.M., B.H.); andLancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, United Kingdom (P.J.L.)
| | - Martine Miquel
- Departments of Chemical Engineering (M.S., R.S., C.D.M.) and Bioinformatics and Genomics, Huck Institutes of the Life Sciences (A.K.), Pennsylvania State University, University Park, Pennsylvania 16802;Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, Centre de Versailles-Grignon, Unité Mixte de Recherche 1318 Institut National de la Recherche Agronomique-Agro-ParisTech, Equipe de Recherce Labellisée, Centre National de la Recherche Scientifique 3559, F-78026 Versailles cedex, France (N.A., L.G., G.C., M.M., Z.L., G.M., B.H.); andLancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, United Kingdom (P.J.L.)
| | - Zhenni Li
- Departments of Chemical Engineering (M.S., R.S., C.D.M.) and Bioinformatics and Genomics, Huck Institutes of the Life Sciences (A.K.), Pennsylvania State University, University Park, Pennsylvania 16802;Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, Centre de Versailles-Grignon, Unité Mixte de Recherche 1318 Institut National de la Recherche Agronomique-Agro-ParisTech, Equipe de Recherce Labellisée, Centre National de la Recherche Scientifique 3559, F-78026 Versailles cedex, France (N.A., L.G., G.C., M.M., Z.L., G.M., B.H.); andLancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, United Kingdom (P.J.L.)
| | - Gregory Mouille
- Departments of Chemical Engineering (M.S., R.S., C.D.M.) and Bioinformatics and Genomics, Huck Institutes of the Life Sciences (A.K.), Pennsylvania State University, University Park, Pennsylvania 16802;Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, Centre de Versailles-Grignon, Unité Mixte de Recherche 1318 Institut National de la Recherche Agronomique-Agro-ParisTech, Equipe de Recherce Labellisée, Centre National de la Recherche Scientifique 3559, F-78026 Versailles cedex, France (N.A., L.G., G.C., M.M., Z.L., G.M., B.H.); andLancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, United Kingdom (P.J.L.)
| | - Peter J Lea
- Departments of Chemical Engineering (M.S., R.S., C.D.M.) and Bioinformatics and Genomics, Huck Institutes of the Life Sciences (A.K.), Pennsylvania State University, University Park, Pennsylvania 16802;Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, Centre de Versailles-Grignon, Unité Mixte de Recherche 1318 Institut National de la Recherche Agronomique-Agro-ParisTech, Equipe de Recherce Labellisée, Centre National de la Recherche Scientifique 3559, F-78026 Versailles cedex, France (N.A., L.G., G.C., M.M., Z.L., G.M., B.H.); andLancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, United Kingdom (P.J.L.)
| | - Bertrand Hirel
- Departments of Chemical Engineering (M.S., R.S., C.D.M.) and Bioinformatics and Genomics, Huck Institutes of the Life Sciences (A.K.), Pennsylvania State University, University Park, Pennsylvania 16802;Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, Centre de Versailles-Grignon, Unité Mixte de Recherche 1318 Institut National de la Recherche Agronomique-Agro-ParisTech, Equipe de Recherce Labellisée, Centre National de la Recherche Scientifique 3559, F-78026 Versailles cedex, France (N.A., L.G., G.C., M.M., Z.L., G.M., B.H.); andLancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, United Kingdom (P.J.L.)
| | - Costas D Maranas
- Departments of Chemical Engineering (M.S., R.S., C.D.M.) and Bioinformatics and Genomics, Huck Institutes of the Life Sciences (A.K.), Pennsylvania State University, University Park, Pennsylvania 16802;Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, Centre de Versailles-Grignon, Unité Mixte de Recherche 1318 Institut National de la Recherche Agronomique-Agro-ParisTech, Equipe de Recherce Labellisée, Centre National de la Recherche Scientifique 3559, F-78026 Versailles cedex, France (N.A., L.G., G.C., M.M., Z.L., G.M., B.H.); andLancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, United Kingdom (P.J.L.)
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