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Zhang Y, Wang N, He C, Gao Z, Chen G. Comparative transcriptome analysis reveals major genes, transcription factors and biosynthetic pathways associated with leaf senescence in rice under different nitrogen application. BMC PLANT BIOLOGY 2024; 24:419. [PMID: 38760728 PMCID: PMC11102181 DOI: 10.1186/s12870-024-05129-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 05/10/2024] [Indexed: 05/19/2024]
Abstract
BACKGROUND Rice (Oryza sativa L.) is one of the most important food crops in the world and the application of nitrogen fertilizer is an effective means of ensuring stable and high rice yields. However, excessive application of nitrogen fertilizer not only causes a decline in the quality of rice, but also leads to a series of environmental costs. Nitrogen reutilization is closely related to leaf senescence, and nitrogen deficiency will lead to early functional leaf senescence, whereas moderate nitrogen application will help to delay leaf senescence and promote the production of photosynthetic assimilation products in leaves to achieve yield increase. Therefore, it is important to explore the mechanism by which nitrogen affects rice senescence, to search for genes that are tolerant to low nitrogen, and to delay the premature senescence of rice functional leaves. RESULTS The present study was investigated the transcriptional changes in flag leaves between full heading and mature grain stages of rice (O. sativa) sp. japonica 'NanGeng 5718' under varying nitrogen (N) application: 0 kg/ha (no nitrogen; 0N), 240 kg/ha (moderate nitrogen; MN), and 300 kg/ha (high nitrogen; HN). Compared to MN condition, a total of 10427 and 8177 differentially expressed genes (DEGs) were detected in 0N and HN, respectively. We selected DEGs with opposite expression trends under 0N and HN conditions for GO and KEGG analyses to reveal the molecular mechanisms of nitrogen response involving DEGs. We confirmed that different N applications caused reprogramming of plant hormone signal transduction, glycolysis/gluconeogenesis, ascorbate and aldarate metabolism and photosynthesis pathways in regulating leaf senescence. Most DEGs of the jasmonic acid, ethylene, abscisic acid and salicylic acid metabolic pathways were up-regulated under 0N condition, whereas DEGs related to cytokinin and ascorbate metabolic pathways were induced in HN. Major transcription factors include ERF, WRKY, NAC and bZIP TF families have similar expression patterns which were induced under N starvation condition. CONCLUSION Our results revealed that different nitrogen levels regulate rice leaf senescence mainly by affecting hormone levels and ascorbic acid biosynthesis. Jasmonic acid, ethylene, abscisic acid and salicylic acid promote early leaf senescence under low nitrogen condition, ethylene and ascorbate delay senescence under high nitrogen condition. In addition, ERF, WRKY, NAC and bZIP TF families promote early leaf senescence. The relevant genes can be used as candidate genes for the regulation of senescence. The results will provide gene reference for further genomic studies and new insights into the gene functions, pathways and transcription factors of N level regulates leaf senescence in rice, thereby improving NUE and reducing the adverse effects of over-application of N.
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Affiliation(s)
- Yafang Zhang
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Ning Wang
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Chenggong He
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Zhiping Gao
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
| | - Guoxiang Chen
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
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Grzybowski MW, Zwiener M, Jin H, Wijewardane NK, Atefi A, Naldrett MJ, Alvarez S, Ge Y, Schnable JC. Variation in morpho-physiological and metabolic responses to low nitrogen stress across the sorghum association panel. BMC PLANT BIOLOGY 2022; 22:433. [PMID: 36076172 PMCID: PMC9461132 DOI: 10.1186/s12870-022-03823-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 09/05/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Access to biologically available nitrogen is a key constraint on plant growth in both natural and agricultural settings. Variation in tolerance to nitrogen deficit stress and productivity in nitrogen limited conditions exists both within and between plant species. However, our understanding of changes in different phenotypes under long term low nitrogen stress and their impact on important agronomic traits, such as yield, is still limited. RESULTS Here we quantified variation in the metabolic, physiological, and morphological responses of a sorghum association panel assembled to represent global genetic diversity to long term, nitrogen deficit stress and the relationship of these responses to grain yield under both conditions. Grain yield exhibits substantial genotype by environment interaction while many other morphological and physiological traits exhibited consistent responses to nitrogen stress across the population. Large scale nontargeted metabolic profiling for a subset of lines in both conditions identified a range of metabolic responses to long term nitrogen deficit stress. Several metabolites were associated with yield under high and low nitrogen conditions. CONCLUSION Our results highlight that grain yield in sorghum, unlike many morpho-physiological traits, exhibits substantial variability of genotype specific responses to long term low severity nitrogen deficit stress. Metabolic response to long term nitrogen stress shown higher proportion of variability explained by genotype specific responses than did morpho-pysiological traits and several metabolites were correlated with yield. This suggest, that it might be possible to build predictive models using metabolite abundance to estimate which sorghum genotypes will exhibit greater or lesser decreases in yield in response to nitrogen deficit, however further research needs to be done to evaluate such model.
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Affiliation(s)
- Marcin W Grzybowski
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, USA.
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, USA.
- Department of Plant Molecular Ecophysiology, Institute of Plant Experimental Biology and Biotechnology, Faculty of Biology, University of Warsaw, Warsw, Poland.
| | - Mackenzie Zwiener
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, USA
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, USA
| | - Hongyu Jin
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, USA
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, USA
| | - Nuwan K Wijewardane
- Department of Agricultural and Biological Engineering, Mississippi State University, Starkville, USA
| | - Abbas Atefi
- Department of Biological Systems Engineering, University of Nebraska-Lincoln, Lincoln, USA
- California Strawberry Commission, San Luis Obispo, USA
| | - Michael J Naldrett
- Proteomics and Metabolomics Facility, Nebraska Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, USA
| | - Sophie Alvarez
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, USA
- Proteomics and Metabolomics Facility, Nebraska Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, USA
| | - Yufeng Ge
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, USA
- Department of Agricultural and Biological Engineering, Mississippi State University, Starkville, USA
| | - James C Schnable
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, USA.
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, USA.
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Tantray AY, Hazzazi Y, Ahmad A. Physiological, Agronomical, and Proteomic Studies Reveal Crucial Players in Rice Nitrogen Use Efficiency under Low Nitrogen Supply. Int J Mol Sci 2022; 23:ijms23126410. [PMID: 35742855 PMCID: PMC9224494 DOI: 10.3390/ijms23126410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 06/03/2022] [Accepted: 06/06/2022] [Indexed: 11/26/2022] Open
Abstract
Excessive use of nitrogenous fertilizers to enhance rice productivity has become a significant source of nitrogen (N) pollution and reduced sustainable agriculture. However, little information about the physiology of different growth stages, agronomic traits, and associated genetic bases of N use efficiency (NUE) are available at low-N supply. Two rice (Oryza sativa L.) cultivars were grown with optimum N (120 kg ha−1) and low N (60 kg ha−1) supply. Six growth stages were analyzed to measure the growth and physiological traits, as well as the differential proteomic profiles, of the rice cultivars. Cultivar Panvel outclassed Nagina 22 at low-N supply and exhibited improved growth and physiology at most of the growth stages and agronomic efficiency due to higher N uptake and utilization at low-N supply. On average, photosynthetic rate, chlorophyll content, plant biomass, leaf N content, and grain yield were decreased in cultivar Nagina 22 than Panvel was 8%, 11%, 21%, 19%, and 22%, respectively, under low-N supply. Furthermore, proteome analyses revealed that many proteins were upregulated and downregulated at the different growth stages under low-N supply. These proteins are associated with N and carbon metabolism and other physiological processes. This supports the genotypic differences in photosynthesis, N assimilation, energy stabilization, and rice-protein yield. Our study suggests that enhancing NUE at low-N supply demands distinct modifications in N metabolism and physiological assimilation. The NUE may be regulated by key identified differentially expressed proteins. These proteins might be the targets for improving crop NUE at low-N supply.
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Affiliation(s)
- Aadil Yousuf Tantray
- Department of Botany, Aligarh Muslim University, Aligarh 202002, Uttar Pradesh, India;
| | - Yehia Hazzazi
- School of Biological Sciences, University of Aberdeen, Aberdeen AB24 3UU, UK;
- Biology Department, Faculty of Sciences, Jazan University, Jazan 45142, Saudi Arabia
| | - Altaf Ahmad
- Department of Botany, Aligarh Muslim University, Aligarh 202002, Uttar Pradesh, India;
- Correspondence:
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Meng X, Wang X, Zhang Z, Xiong S, Wei Y, Guo J, Zhang J, Wang L, Ma X, Tegeder M. Transcriptomic, proteomic, and physiological studies reveal key players in wheat nitrogen use efficiency under both high and low nitrogen supply. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:4435-4456. [PMID: 33829261 DOI: 10.1093/jxb/erab153] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 04/02/2021] [Indexed: 06/12/2023]
Abstract
The effective use of available nitrogen (N) to improve crop grain yields provides an important strategy to reduce environmental N pollution and promote sustainable agriculture. However, little is known about the common genetic basis of N use efficiency (NUE) at varying N availability. Two wheat (Triticum aestivum L.) cultivars were grown in the field with high, moderate, and low N supply. Cultivar Zhoumai 27 outperformed Aikang 58 independent of the N supply and showed improved growth, canopy leaf area index, flag leaf surface area, grain number, and yield, and enhanced NUE due to both higher N uptake and utilization efficiency. Further, transcriptome and proteome analyses were performed using flag leaves that provide assimilates for grain growth. The results showed that many genes or proteins that are up- or down-regulated under all N regimes are associated with N and carbon metabolism and transport. This was reinforced by cultivar differences in photosynthesis, assimilate phloem transport, and grain protein/starch yield. Overall, our study establishes that improving NUE at both high and low N supply requires distinct adjustments in leaf metabolism and assimilate partitioning. Identified key genes/proteins may individually or concurrently regulate NUE and are promising targets for maximizing crop NUE irrespective of the N supply.
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Affiliation(s)
- Xiaodan Meng
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, ZhengzhouChina
- College of Agronomy, Henan Agricultural University, ZhengzhouChina
- School of Biological Sciences, Washington State University, Pullman, WAUSA
| | - Xiaochun Wang
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, ZhengzhouChina
| | - Zhiyong Zhang
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, ZhengzhouChina
- College of Agronomy, Henan Agricultural University, ZhengzhouChina
| | - Shuping Xiong
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, ZhengzhouChina
- College of Agronomy, Henan Agricultural University, ZhengzhouChina
| | - Yihao Wei
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, ZhengzhouChina
- College of Agronomy, Henan Agricultural University, ZhengzhouChina
| | - Jianbiao Guo
- College of Agronomy, Henan Agricultural University, ZhengzhouChina
| | - Jie Zhang
- College of Agronomy, Henan Agricultural University, ZhengzhouChina
| | - Lulu Wang
- College of Agronomy, Henan Agricultural University, ZhengzhouChina
| | - Xinming Ma
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, ZhengzhouChina
- College of Agronomy, Henan Agricultural University, ZhengzhouChina
| | - Mechthild Tegeder
- School of Biological Sciences, Washington State University, Pullman, WAUSA
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5
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dos Santos A, do Amaral Júnior AT, Fritsche-Neto R, Kamphorst SH, Ferreira FRA, do Amaral JFT, Vivas JMS, Santos PHAD, de Lima VJ, Khan S, Schmitt KFM, Leite JT, Junior DRDS, Bispo RB, Santos TDO, de Oliveira UA, Guimarães LJM, Rodriguez O. Relative importance of gene effects for nitrogen-use efficiency in popcorn. PLoS One 2019; 14:e0222726. [PMID: 31557221 PMCID: PMC6762054 DOI: 10.1371/journal.pone.0222726] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 09/05/2019] [Indexed: 11/18/2022] Open
Abstract
The objective of this study was to evaluate the effects of additive and non-additive genes on the efficiency of nitrogen (N) use and N responsiveness in inbred popcorn lines. The parents, hybrids and reciprocal crosses were evaluated in a 10x10 triple lattice design at two sites and two levels of N availability. To establish different N levels in the two experiments, fertilization was carried out at sowing, according to soil analysis reports. However, for the experiments with ideal nitrogen availability, N was sidedressed according to the crop requirement, whereas for the N-poor experiments sidedressing consisted of 30% of that applied in the N-rich environment. Two indices were evaluated, the Harmonic Mean of the Relative Performance (HMRP) and Agronomic Efficiency under Low Nitrogen Availability (AELN), both based on grain yield at both N levels. Both additive and non-additive gene effects were important for selection for N-use efficiency. Moreover, there was allelic complementarity between the lines and a reciprocal effect for N-use efficiency, indicating the importance of the choice of the parents used as male or female. The best hybrids were obtained from inbred popcorn lines with contrasting N-use efficiency and N responsiveness.
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Affiliation(s)
- Adriano dos Santos
- Laboratório de Melhoramento Genético Vegetal, Centro de Ciências e Tecnologias Agropecuárias, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, RJ, Brazil
| | - Antônio Teixeira do Amaral Júnior
- Laboratório de Melhoramento Genético Vegetal, Centro de Ciências e Tecnologias Agropecuárias, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, RJ, Brazil
- * E-mail:
| | - Roberto Fritsche-Neto
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz (ESALQ), Piracicaba, SP, Brazil
| | - Samuel Henrique Kamphorst
- Laboratório de Melhoramento Genético Vegetal, Centro de Ciências e Tecnologias Agropecuárias, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, RJ, Brazil
| | - Fernando Rafael Alves Ferreira
- Laboratório de Melhoramento Genético Vegetal, Centro de Ciências e Tecnologias Agropecuárias, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, RJ, Brazil
| | - José Francisco Teixeira do Amaral
- Departamento de Engenharia Rural, Centro de Ciências Agrárias e Engenharias, Universidade Federal do Espírito Santo (UFES), Alegre, ES, Brazil
| | - Janieli Maganha Silva Vivas
- Laboratório de Melhoramento Genético Vegetal, Centro de Ciências e Tecnologias Agropecuárias, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, RJ, Brazil
| | - Pedro Henrique Araújo Diniz Santos
- Laboratório de Melhoramento Genético Vegetal, Centro de Ciências e Tecnologias Agropecuárias, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, RJ, Brazil
| | - Valter Jário de Lima
- Laboratório de Melhoramento Genético Vegetal, Centro de Ciências e Tecnologias Agropecuárias, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, RJ, Brazil
| | - Shahid Khan
- Laboratório de Melhoramento Genético Vegetal, Centro de Ciências e Tecnologias Agropecuárias, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, RJ, Brazil
| | - Kátia Fabiane Medeiros Schmitt
- Laboratório de Melhoramento Genético Vegetal, Centro de Ciências e Tecnologias Agropecuárias, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, RJ, Brazil
| | - Jhean Torres Leite
- Laboratório de Melhoramento Genético Vegetal, Centro de Ciências e Tecnologias Agropecuárias, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, RJ, Brazil
| | - Divino Rosa dos Santos Junior
- Laboratório de Melhoramento Genético Vegetal, Centro de Ciências e Tecnologias Agropecuárias, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, RJ, Brazil
| | - Rosimeire Barboza Bispo
- Laboratório de Melhoramento Genético Vegetal, Centro de Ciências e Tecnologias Agropecuárias, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, RJ, Brazil
| | - Talles de Oliveira Santos
- Laboratório de Melhoramento Genético Vegetal, Centro de Ciências e Tecnologias Agropecuárias, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, RJ, Brazil
| | - Uéliton Alves de Oliveira
- Laboratório de Melhoramento Genético Vegetal, Centro de Ciências e Tecnologias Agropecuárias, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, RJ, Brazil
| | - Lauro José Moreira Guimarães
- Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA), Centro Nacional de Pesquisa de Milho e Sorgo, Sete Lagoas, MG, Brazil
| | - Oscar Rodriguez
- Department of Agronomy and Horticulture, University of Nebraska, Nebraska, United States of America
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Silva IT, Abbaraju HKR, Fallis LP, Liu H, Lee M, Dhugga KS. Biochemical and genetic analyses of N metabolism in maize testcross seedlings: 2. Roots. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131. [PMID: 29541827 PMCID: PMC5945762 DOI: 10.1007/s00122-018-3071-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Intracellular factors differentially affected enzyme activities of N assimilation in the roots of maize testcrosses where alanine aminotransferase and glutamate synthase were the main enzymes regulating the levels of glutamate. N is a key macronutrient for plant growth and development. Breeding maize with improved efficiency in N use could help reduce environmental contamination as well as increase profitability for the farmers. Quantitative trait loci (QTL) mapping of traits related to N metabolism in the root tissue was undertaken in a maize testcross mapping population grown in hydroponic cultures. N concentration was negatively correlated with root and total dry mass. Neither the enzyme activities nor metabolites were appreciably correlated between the root and leaf tissues. Repeatability measures for most of the enzymes were lower than for dry mass. Weak negative correlations between most of the enzymes and dry mass resulted likely from dilution and suggested the presence of excess of enzyme activities for maximal biomass production. Glutamate synthase and alanine aminotransferase each explained more variation in glutamate concentration than either aspartate aminotransferase or asparagine synthetase whereas glutamine synthetase was inconsequential. Twenty-six QTL were identified across all traits. QTL models explained 7-43% of the variance with no significant epistasis between the QTL. Thirteen candidate genes were identified underlying QTL within 1-LOD confidence intervals. All the candidate genes were located in trans configuration, unlinked or even on different chromosomes, relative to the known genomic positions of the corresponding structural genes. Our results have implications in improving NUE in maize and other crop plants.
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Affiliation(s)
- Ignacio Trucillo Silva
- Department of Agronomy, Iowa State University, Ames, IA, 50011, USA
- Global Breeding and Marker Technologies, Dupont Pioneer, 5000, Córdoba, Argentina
| | - Hari Kishan R Abbaraju
- Genetic Discovery Group, DuPont Pioneer, Johnston, IA, 50131, USA
- AVX Corporation, One AVX Blvd., Fountain Inn, SC, 29644, USA
| | - Lynne P Fallis
- Genetic Discovery Group, DuPont Pioneer, Johnston, IA, 50131, USA
| | - Hongjun Liu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, China
| | - Michael Lee
- Department of Agronomy, Iowa State University, Ames, IA, 50011, USA.
| | - Kanwarpal S Dhugga
- Genetic Discovery Group, DuPont Pioneer, Johnston, IA, 50131, USA.
- Genetic Resources Program, International Center for Maize and Wheat Improvement (CIMMYT), 56237, El Batan, Texcoco, Mexico.
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7
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Hu X, Wang H, Li K, Wu Y, Liu Z, Huang C. Genome-wide proteomic profiling reveals the role of dominance protein expression in heterosis in immature maize ears. Sci Rep 2017; 7:16130. [PMID: 29170427 PMCID: PMC5700959 DOI: 10.1038/s41598-017-15985-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 11/06/2017] [Indexed: 01/02/2023] Open
Abstract
Heterosis refers to the phenomenon in which hybrid progeny show superior performance relative to their parents. Early maize ear development shows strong heterosis in ear architecture traits and greatly affects grain yield. To explore the underlying molecular mechanisms, genome-wide proteomics of immature ears of maize hybrid ZD909 and its parents were analyzed using tandem mass tag (TMT) technology. A total of 9,713 proteins were identified in all three genotypes. Among them, 3,752 (38.6%) proteins were differentially expressed between ZD909 and its parents. Multiple modes of protein action were discovered in the hybrid, while dominance expression patterns accounted for 63.6% of the total differentially expressed proteins (DEPs). Protein pathway enrichment analysis revealed that high parent dominance proteins mainly participated in carbon metabolism and nitrogen assimilation processes. Our results suggested that the dominant expression of favorable alleles related to C/N metabolism in the hybrid may be essential for ZD909 ear growth and heterosis formation. Integrated analysis of proteomic and quantitative trait locus (QTL) data further support our DEP identification and provide useful information for the discovery of genes associated with ear development. Our study provides comprehensive insight into the molecular mechanisms underlying heterosis in immature maize ears from a proteomic perspective.
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Affiliation(s)
- Xiaojiao Hu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Engineering Laboratory for Crop Molecular Breeding, Beijing, 100081, China
| | - Hongwu Wang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Engineering Laboratory for Crop Molecular Breeding, Beijing, 100081, China
| | - Kun Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Engineering Laboratory for Crop Molecular Breeding, Beijing, 100081, China
| | - Yujin Wu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Engineering Laboratory for Crop Molecular Breeding, Beijing, 100081, China
| | - Zhifang Liu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Engineering Laboratory for Crop Molecular Breeding, Beijing, 100081, China.
| | - Changling Huang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Engineering Laboratory for Crop Molecular Breeding, Beijing, 100081, China.
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8
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Saiz-Fernández I, De Diego N, Brzobohatý B, Muñoz-Rueda A, Lacuesta M. The imbalance between C and N metabolism during high nitrate supply inhibits photosynthesis and overall growth in maize (Zea mays L.). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2017; 120:213-222. [PMID: 29059604 DOI: 10.1016/j.plaphy.2017.10.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 10/05/2017] [Accepted: 10/09/2017] [Indexed: 05/22/2023]
Abstract
Nitrogen (N) is an important regulator of photosynthetic carbon (C) flow in plants, and an adequate balance between N and C metabolism is needed for correct plant development. However, an excessive N supply can alter this balance and cause changes in specific organic compounds associated with primary and secondary metabolism, including plant growth regulators. In previous work, we observed that high nitrate supply (15 mM) to maize plants led to a decrease in leaf expansion and overall biomass production, when compared with low nitrate supply (5 mM). Thus, the aim of this work is to study how overdoses of nitrate can affect photosynthesis and plant development. The results show that high nitrate doses greatly increased amino acid production, which led to a decrease in the concentration of 2-oxoglutarate, the main source of C skeletons for N assimilation. The concentration of 1-aminocyclopropane-1-carboxylic acid (and possibly its product, ethylene) also rose in high nitrate plants, leading to a decrease in leaf expansion, reducing the demand for photoassimilates by the growing tissues and causing the accumulation of sugars in source leaves. This accumulation of sugars, together with the decrease in 2-oxoglutarate levels and the reduction in chlorophyll concentration, decreased plant photosynthetic rates. This work provides new insights into how high nitrate concentration alters the balance between C and N metabolism, reducing photosynthetic rates and disrupting whole plant development. These findings are particularly relevant since negative effects of nitrate in contexts other than root growth have rarely been studied.
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Affiliation(s)
- Iñigo Saiz-Fernández
- Department of Plant Biology and Ecology, Faculty of Pharmacy, University of the Basque Country UPV/EHU, E-01006, Vitoria-Gasteiz, Spain; Laboratory of Plant Molecular Biology, Institute of Biophysics AS CR, CEITEC - Central European Institute of Technology, Phytophthora Research Centre, Faculty of Agronomy, Mendel University in Brno, Zemědělská 1, CZ-613 00, Brno, Czech Republic.
| | - Nuria De Diego
- Department of Plant Biology and Ecology, Faculty of Pharmacy, University of the Basque Country UPV/EHU, E-01006, Vitoria-Gasteiz, Spain; Department of Chemical Biology and Genetics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, CZ-783 71, Olomouc, Czech Republic
| | - Břetislav Brzobohatý
- Laboratory of Plant Molecular Biology, Institute of Biophysics AS CR, CEITEC - Central European Institute of Technology, Phytophthora Research Centre, Faculty of Agronomy, Mendel University in Brno, Zemědělská 1, CZ-613 00, Brno, Czech Republic
| | - Alberto Muñoz-Rueda
- Department of Plant Biology and Ecology, Faculty of Sciences and Technology, University of the Basque Country UPV/EHU, E-48080, Leioa, Spain
| | - Maite Lacuesta
- Department of Plant Biology and Ecology, Faculty of Pharmacy, University of the Basque Country UPV/EHU, E-01006, Vitoria-Gasteiz, Spain
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9
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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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10
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Martinez AK, Soriano JM, Tuberosa R, Koumproglou R, Jahrmann T, Salvi S. Yield QTLome distribution correlates with gene density in maize. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 242:300-309. [PMID: 26566847 DOI: 10.1016/j.plantsci.2015.09.022] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 09/22/2015] [Accepted: 09/23/2015] [Indexed: 05/09/2023]
Abstract
The genetic control of yield and related traits in maize has been addressed by many quantitative trait locus (QTL) studies, which have produced a wealth of QTL information, also known as QTLome. In this study, we assembled a yield QTLome database and carried out QTL meta-analysis based on 44 published studies, representing 32 independent mapping populations and 49 parental lines. A total of 808 unique QTLs were condensed to 84 meta-QTLs and were projected on the 10 maize chromosomes. Seventy-four percent of QTLs showed a proportion of phenotypic variance explained (PVE) smaller than 10% confirming the high genetic complexity of grain yield. Yield QTLome projection on the genetic map suggested pericentromeric enrichment of QTLs. Conversely, pericentromeric depletion of QTLs was observed when the physical map was considered, suggesting gene density as the main driver of yield QTL distribution on chromosomes. Dominant and overdominant yield QTLs did not distribute differently from additive effect QTLs.
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Affiliation(s)
- Ana Karine Martinez
- Department of Agricultural Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy
| | - Jose Miguel Soriano
- Department of Agricultural Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy; Field Crops Programme, IRTA (Institute for Food and Agricultural Research and Technology), 25198 Lleida, Spain
| | - Roberto Tuberosa
- Department of Agricultural Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy
| | | | | | - Silvio Salvi
- Department of Agricultural Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy.
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11
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Garnett T, Plett D, Heuer S, Okamoto M. Genetic approaches to enhancing nitrogen-use efficiency (NUE) in cereals: challenges and future directions. FUNCTIONAL PLANT BIOLOGY : FPB 2015; 42:921-941. [PMID: 32480734 DOI: 10.1071/fp15025] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 06/24/2015] [Indexed: 05/03/2023]
Abstract
Over 100million tonnes of nitrogen (N) fertiliser are applied globally each year to maintain high yields in agricultural crops. The rising price of N fertilisers has made them a major cost for farmers. Inefficient use of N fertiliser leads to substantial environmental problems through contamination of air and water resources and can be a significant economic cost. Consequently, there is considerable need to improve the way N fertiliser is used in farming systems. The efficiency with which crops use applied N fertiliser - the nitrogen-use efficiency (NUE) - is currently quite low for cereals. This is the case in both high yielding environments and lower yielding environments characteristic of cereal growing regions of Australia. Multiple studies have attempted to identify the genetic basis of NUE, but the utility of the results is limited because of the complex nature of the trait and the magnitude of genotype by environment interaction. Transgenic approaches have been applied to improve plant NUE but with limited success, due, in part, to a combination of the complexity of the trait but also due to lack of accurate phenotyping methods. This review documents these two approaches and suggests future directions in improving cereal NUE with a focus on the Australian cereal industry.
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Affiliation(s)
- Trevor Garnett
- Australian Centre for Plant Functional Genomics, School of Agriculture Food and Wine, University of Adelaide, Adelaide, SA 5064, Australia
| | - Darren Plett
- Australian Centre for Plant Functional Genomics, School of Agriculture Food and Wine, University of Adelaide, Adelaide, SA 5064, Australia
| | - Sigrid Heuer
- Australian Centre for Plant Functional Genomics, School of Agriculture Food and Wine, University of Adelaide, Adelaide, SA 5064, Australia
| | - Mamoru Okamoto
- Australian Centre for Plant Functional Genomics, School of Agriculture Food and Wine, University of Adelaide, Adelaide, SA 5064, Australia
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12
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Valluru R, Reynolds MP, Lafarge T. Food security through translational biology between wheat and rice. Food Energy Secur 2015. [DOI: 10.1002/fes3.71] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Ravi Valluru
- Global Wheat Program International Maize and Wheat Improvement Center (CIMMYT) El Batan Mexico
| | - Matthew P. Reynolds
- Global Wheat Program International Maize and Wheat Improvement Center (CIMMYT) El Batan Mexico
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13
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Li P, Chen F, Cai H, Liu J, Pan Q, Liu Z, Gu R, Mi G, Zhang F, Yuan L. A genetic relationship between nitrogen use efficiency and seedling root traits in maize as revealed by QTL analysis. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:3175-88. [PMID: 25873660 PMCID: PMC4449538 DOI: 10.1093/jxb/erv127] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
That root system architecture (RSA) has an essential role in nitrogen acquisition is expected in maize, but the genetic relationship between RSA and nitrogen use efficiency (NUE) traits remains to be elucidated. Here, the genetic basis of RSA and NUE traits was investigated in maize using a recombination inbred line population that was derived from two lines contrasted for both traits. Under high-nitrogen and low-nitrogen conditions, 10 NUE- and 9 RSA-related traits were evaluated in four field environments and three hydroponic experiments, respectively. In contrast to nitrogen utilization efficiency (NutE), nitrogen uptake efficiency (NupE) had significant phenotypic correlations with RSA, particularly the traits of seminal roots (r = 0.15-0.31) and crown roots (r = 0.15-0.18). A total of 331 quantitative trait loci (QTLs) were detected, including 184 and 147 QTLs for NUE- and RSA-related traits, respectively. These QTLs were assigned into 64 distinct QTL clusters, and ~70% of QTLs for nitrogen-efficiency (NUE, NupE, and NutE) coincided in clusters with those for RSA. Five important QTLs clusters at the chromosomal regions bin1.04, 2.04, 3.04, 3.05/3.06, and 6.07/6.08 were found in which QTLs for both traits had favourable effects from alleles coming from the large-rooted and high-NupE parent. Introgression of these QTL clusters in the advanced backcross-derived lines conferred mean increases in grain yield of ~14.8% for the line per se and ~15.9% in the testcross. These results reveal a significant genetic relationship between RSA and NUE traits, and uncover the most promising genomic regions for marker-assisted selection of RSA to improve NUE in maize.
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Affiliation(s)
- Pengcheng Li
- Key Laboratory of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural University, Beijing, China 100193
| | - Fanjun Chen
- Key Laboratory of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural University, Beijing, China 100193
| | - Hongguang Cai
- Key Laboratory of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural University, Beijing, China 100193
| | - Jianchao Liu
- Key Laboratory of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural University, Beijing, China 100193
| | - Qingchun Pan
- Key Laboratory of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural University, Beijing, China 100193
| | - Zhigang Liu
- Key Laboratory of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural University, Beijing, China 100193
| | - Riliang Gu
- Key Laboratory of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural University, Beijing, China 100193
| | - Guohua Mi
- Key Laboratory of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural University, Beijing, China 100193
| | - Fusuo Zhang
- Key Laboratory of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural University, Beijing, China 100193
| | - Lixing Yuan
- Key Laboratory of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural University, Beijing, China 100193
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14
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Coneva V, Simopoulos C, Casaretto JA, El-Kereamy A, Guevara DR, Cohn J, Zhu T, Guo L, Alexander DC, Bi YM, McNicholas PD, Rothstein SJ. Metabolic and co-expression network-based analyses associated with nitrate response in rice. BMC Genomics 2014; 15:1056. [PMID: 25471115 PMCID: PMC4301927 DOI: 10.1186/1471-2164-15-1056] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 11/27/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Understanding gene expression and metabolic re-programming that occur in response to limiting nitrogen (N) conditions in crop plants is crucial for the ongoing progress towards the development of varieties with improved nitrogen use efficiency (NUE). To unravel new details on the molecular and metabolic responses to N availability in a major food crop, we conducted analyses on a weighted gene co-expression network and metabolic profile data obtained from leaves and roots of rice plants adapted to sufficient and limiting N as well as after shifting them to limiting (reduction) and sufficient (induction) N conditions. RESULTS A gene co-expression network representing clusters of rice genes with similar expression patterns across four nitrogen conditions and two tissue types was generated. The resulting 18 clusters were analyzed for enrichment of significant gene ontology (GO) terms. Four clusters exhibited significant correlation with limiting and reducing nitrate treatments. Among the identified enriched GO terms, those related to nucleoside/nucleotide, purine and ATP binding, defense response, sugar/carbohydrate binding, protein kinase activities, cell-death and cell wall enzymatic activity are enriched. Although a subset of functional categories are more broadly associated with the response of rice organs to limiting N and N reduction, our analyses suggest that N reduction elicits a response distinguishable from that to adaptation to limiting N, particularly in leaves. This observation is further supported by metabolic profiling which shows that several compounds in leaves change proportionally to the nitrate level (i.e. higher in sufficient N vs. limiting N) and respond with even higher levels when the nitrate level is reduced. Notably, these compounds are directly involved in N assimilation, transport, and storage (glutamine, asparagine, glutamate and allantoin) and extend to most amino acids. Based on these data, we hypothesize that plants respond by rapidly mobilizing stored vacuolar nitrate when N deficit is perceived, and that the response likely involves phosphorylation signal cascades and transcriptional regulation. CONCLUSIONS The co-expression network analysis and metabolic profiling performed in rice pinpoint the relevance of signal transduction components and regulation of N mobilization in response to limiting N conditions and deepen our understanding of N responses and N use in crops.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Steven J Rothstein
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada.
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15
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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: 37] [Impact Index Per Article: 3.7] [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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16
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Bi YM, Meyer A, Downs GS, Shi X, El-Kereamy A, Lukens L, Rothstein SJ. High throughput RNA sequencing of a hybrid maize and its parents shows different mechanisms responsive to nitrogen limitation. BMC Genomics 2014; 15:77. [PMID: 24472600 PMCID: PMC3912931 DOI: 10.1186/1471-2164-15-77] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Accepted: 01/25/2014] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Development of crop varieties with high nitrogen use efficiency (NUE) is crucial for minimizing N loss, reducing environmental pollution and decreasing input cost. Maize is one of the most important crops cultivated worldwide and its productivity is closely linked to the amount of fertilizer used. A survey of the transcriptomes of shoot and root tissues of a maize hybrid line and its two parental inbred lines grown under sufficient and limiting N conditions by mRNA-Seq has been conducted to have a better understanding of how different maize genotypes respond to N limitation. RESULTS A different set of genes were found to be N-responsive in the three genotypes. Many biological processes important for N metabolism such as the cellular nitrogen compound metabolic process and the cellular amino acid metabolic process were enriched in the N-responsive gene list from the hybrid shoots but not from the parental lines' shoots. Coupled to this, sugar, carbohydrate, monosaccharide, glucose, and sorbitol transport pathways were all up-regulated in the hybrid, but not in the parents under N limitation. Expression patterns also differed between shoots and roots, such as the up-regulation of the cytokinin degradation pathway in the shoots of the hybrid and down-regulation of that pathway in the roots. The change of gene expression under N limitation in the hybrid resembled the parent with the higher NUE trait. The transcript abundances of alleles derived from each parent were estimated using polymorphic sites in mapped reads in the hybrid. While there were allele abundance differences, there was no correlation between these and the expression differences seen between the hybrid and the two parents. CONCLUSIONS Gene expression in two parental inbreds and the corresponding hybrid line in response to N limitation was surveyed using the mRNA-Seq technology. The data showed that the three genotypes respond very differently to N-limiting conditions, and the hybrid clearly has a unique expression pattern compared to its parents. Our results expand our current understanding of N responses and will help move us forward towards effective strategies to improve NUE and enhance crop production.
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Affiliation(s)
| | | | | | | | | | | | - Steven J Rothstein
- Department of Molecular and Cellular Biology, University of Guelph, N1G 2 W1 Guelph, ON, Canada.
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Amiour N, Imbaud S, Clément G, Agier N, Zivy M, Valot B, Balliau T, Armengaud P, Quilleré I, Cañas R, Tercet-Laforgue T, Hirel B. The use of metabolomics integrated with transcriptomic and proteomic studies for identifying key steps involved in the control of nitrogen metabolism in crops such as maize. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:5017-33. [PMID: 22936829 DOI: 10.1093/jxb/ers186] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Linking plant phenotype to gene and protein expression and also to metabolite synthesis and accumulation is one of the main challenges for improving agricultural production worldwide. Such a challenge is particularly relevant to crop nitrogen use efficiency (NUE). Here, the differences in leaf gene transcript, protein, and metabolite accumulation in maize subjected to long-term nitrogen (N)-deficient growth conditions at two important stages of plant development have been studied. The impact of N deficiency was examined at the transcriptomic, proteomic, and metabolomic levels. It was found that a number of key plant biological functions were either up- or down-regulated when N was limiting, including major alterations to photosynthesis, carbon (C) metabolism, and, to a lesser extent, downstream metabolic pathways. It was also found that the impact of the N deficiency stress resembled the response of plants to a number of other biotic and abiotic stresses, in terms of transcript, protein, and metabolite accumulation. The genetic and metabolic alterations were different during the N assimilation and the grain-filling period, indicating that plant development is an important component for identifying the key elements involved in the control of plant NUE. It was also found that integration of the three 'omics' studies is not straightforward, since different levels of regulation seem to occur in a stepwise manner from gene expression to metabolite accumulation. The potential use of these 'omics' studies is discussed with a view to improve our understanding of whole plant nitrogen economics, which should have applications in breeding and agronomy.
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Affiliation(s)
- Nardjis Amiour
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, Centre de Versailles-Grignon, UR 511, Route de St Cyr, F-78026 Versailles Cedex, France
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