1
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Zhang Z, Gomes Viana JP, Zhang B, Walden KKO, Müller Paul H, Moose SP, Morris GP, Daum C, Barry KW, Shakoor N, Hudson ME. Major impacts of widespread structural variation on sorghum. Genome Res 2024; 34:286-299. [PMID: 38479835 PMCID: PMC10984582 DOI: 10.1101/gr.278396.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 01/22/2024] [Indexed: 03/22/2024]
Abstract
Genetic diversity is critical to crop breeding and improvement, and dissection of the genomic variation underlying agronomic traits can both assist breeding and give insight into basic biological mechanisms. Although recent genome analyses in plants reveal many structural variants (SVs), most current studies of crop genetic variation are dominated by single-nucleotide polymorphisms (SNPs). The extent of the impact of SVs on global trait variation, as well as their utility in genome-wide selection, is not yet understood. In this study, we built an SV data set based on whole-genome resequencing of diverse sorghum lines (n = 363), validated the correlation of photoperiod sensitivity and variety type, and identified SV hotspots underlying the divergent evolution of cellulosic and sweet sorghum. In addition, we showed the complementary contribution of SVs for heritability of traits related to sorghum adaptation. Importantly, inclusion of SV polymorphisms in association studies revealed genotype-phenotype associations not observed with SNPs alone. Three-way genome-wide association studies (GWAS) based on whole-genome SNP, SV, and integrated SNP + SV data sets showed substantial associations between SVs and sorghum traits. The addition of SVs to GWAS substantially increased heritability estimates for some traits, indicating their important contribution to functional allelic variation at the genome level. Our discovery of the widespread impacts of SVs on heritable gene expression variation could render a plausible mechanism for their disproportionate impact on phenotypic variation. This study expands our knowledge of SVs and emphasizes the extensive impacts of SVs on sorghum.
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Affiliation(s)
- Zhihai Zhang
- DOE Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Joao Paulo Gomes Viana
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Bosen Zhang
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Kimberly K O Walden
- High Performance Computing in Biology, Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Hans Müller Paul
- DOE Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Stephen P Moose
- DOE Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Geoffrey P Morris
- Department of Soil and Crop Science, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Chris Daum
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Kerrie W Barry
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Nadia Shakoor
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
| | - Matthew E Hudson
- DOE Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA;
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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2
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Fortunato S, Nigro D, Lasorella C, Marcotuli I, Gadaleta A, de Pinto MC. The Role of Glutamine Synthetase (GS) and Glutamate Synthase (GOGAT) in the Improvement of Nitrogen Use Efficiency in Cereals. Biomolecules 2023; 13:1771. [PMID: 38136642 PMCID: PMC10742212 DOI: 10.3390/biom13121771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023] Open
Abstract
Cereals are the most broadly produced crops and represent the primary source of food worldwide. Nitrogen (N) is a critical mineral nutrient for plant growth and high yield, and the quality of cereal crops greatly depends on a suitable N supply. In the last decades, a massive use of N fertilizers has been achieved in the desire to have high yields of cereal crops, leading to damaging effects for the environment, ecosystems, and human health. To ensure agricultural sustainability and the required food source, many attempts have been made towards developing cereal crops with a more effective nitrogen use efficiency (NUE). NUE depends on N uptake, utilization, and lastly, combining the capability to assimilate N into carbon skeletons and remobilize the N assimilated. The glutamine synthetase (GS)/glutamate synthase (GOGAT) cycle represents a crucial metabolic step of N assimilation, regulating crop yield. In this review, the physiological and genetic studies on GS and GOGAT of the main cereal crops will be examined, giving emphasis on their implications in NUE.
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Affiliation(s)
- Stefania Fortunato
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, Via Orabona 4, 70125 Bari, Italy; (S.F.)
| | - Domenica Nigro
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Via Orabona 4, 70125 Bari, Italy; (D.N.); (I.M.)
| | - Cecilia Lasorella
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, Via Orabona 4, 70125 Bari, Italy; (S.F.)
| | - Ilaria Marcotuli
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Via Orabona 4, 70125 Bari, Italy; (D.N.); (I.M.)
| | - Agata Gadaleta
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Via Orabona 4, 70125 Bari, Italy; (D.N.); (I.M.)
| | - Maria Concetta de Pinto
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, Via Orabona 4, 70125 Bari, Italy; (S.F.)
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3
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Zhang C, Wang ST, Li JZ, Feng YL. Molecular bases for the stronger plastic response to high nitrate in the invasive plant Xanthium strumarium compared with its native congener. PLANTA 2023; 258:61. [PMID: 37542564 DOI: 10.1007/s00425-023-04220-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 07/27/2023] [Indexed: 08/07/2023]
Abstract
MAIN CONCLUSION High expressions of nitrate use and photosynthesis-related transcripts contribute to the stronger plasticity to high nitrate for the invader relative to its native congener, which may be driven by hormones. Strong phenotypic plasticity is often considered as one of the main mechanisms underlying exotic plant invasions. However, few studies have been conducted to investigate the related molecular mechanisms. Here, we determined the differences in the plastic responses to high nitrate between the invasive plant X. strumarium and its native congener, and the molecular bases by transcriptome analysis and quantitative real-time PCR validation. Our results showed that the invader had higher plasticity of growth, nitrogen accumulation and photosynthesis in responses to high nitrate than its native congener. Compared with its congener, more N utilization-related transcripts, including nitrate transporter 1/peptide transporter family 6.2 and nitrate reductase 1, were induced by high nitrate in the root of X. strumarium, improving its N utilization ability. More transcripts coding for photosynthetic antenna proteins were also induced by high nitrate in the shoot of X. strumarium, enhancing its photosynthesis. Hormones may be involved in the regulation of the plastic responses to high nitrate in the two species. Our study contributes to understanding the molecular mechanisms underlying the stronger plasticity of the invader in responses to high nitrate, and the potential function of plant hormones in these processes, providing bases for precise control of invasive plants using modern molecular techniques.
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Affiliation(s)
- Chang Zhang
- Liaoning Key Laboratory for Biological Invasions and Global Changes, College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
| | - Shi-Ting Wang
- Liaoning Key Laboratory for Biological Invasions and Global Changes, College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
| | - Jian-Zhi Li
- Liaoning Key Laboratory for Biological Invasions and Global Changes, College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
| | - Yu-Long Feng
- Liaoning Key Laboratory for Biological Invasions and Global Changes, College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China.
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4
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Sun X, Xie F, Chen Y, Guo Z, Dong L, Qin L, Shi Z, Xiong L, Yuan R, Deng W, Jiang Y. Glutamine synthetase gene PpGS1.1 negatively regulates the powdery mildew resistance in Kentucky bluegrass. HORTICULTURE RESEARCH 2022; 9:uhac196. [PMID: 36415534 PMCID: PMC9677456 DOI: 10.1093/hr/uhac196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 08/26/2022] [Indexed: 05/31/2023]
Abstract
Excessive nitrogen (N) application may induce powdery mildew (PM) in perennial grasses, but the resistance mechanisms to PM remain unclear. This study evaluated the physiological and molecular mechanisms of PM resistance affected by N supplies in Kentucky bluegrass (Poa pratensis L.). Cultivar 'Bluemoon' (N tolerant) and 'Balin' (N sensitive) were treated with low N (0.5 mM), normal N (15 mM), and high N (30 mM) for 21 d in a greenhouse. With increasing N levels, the disease growth was more severe in 'Balin' than in 'Bluemoon'. RNA-seq and weighted gene coexpression network analysis revealed that the PpGS1.1 gene encoding glutamine synthetase was a potential hub gene for PM resistance after comparisons across cultivars and N treatments. The N metabolism pathway was connected with the plant-pathogen interaction pathway via PpGS1.1. The expression of PpGS1.1 in rice protoplasts indicated that the protein was located in the nucleus and cytoplasm. Overexpression of PpGS1.1 in wild-type Kentucky bluegrass increased carbon and N contents, and the transgenic plants became more susceptible to PM with a lower wax density. The most differentially expressed genes (DEGs) for N metabolism were upregulated and DEGs for fatty acid metabolism pathway were downregulated in the overexpression lines. The results elucidated mechanisms of PM resistance in relation to N metabolism in Kentucky bluegrass.
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Affiliation(s)
- Xiaoyang Sun
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | | | | | - Zhixin Guo
- College of Horticulture, Northeast Agricultural University, Harbin, China
| | - Lili Dong
- College of Horticulture, Northeast Agricultural University, Harbin, China
| | - Ligang Qin
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Zhenjie Shi
- College of Horticulture, Northeast Agricultural University, Harbin, China
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Liangbing Xiong
- College of Horticulture, Northeast Agricultural University, Harbin, China
| | - Runli Yuan
- College of Horticulture, Northeast Agricultural University, Harbin, China
| | - Wenjing Deng
- College of Horticulture, Northeast Agricultural University, Harbin, China
| | - Yiwei Jiang
- Department of Agronomy, Purdue University, West Lafayette, IN, USA
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Yang F, Zhang J, Zhao Y, Liu Q, Islam S, Yang W, Ma W. Wheat glutamine synthetase TaGSr-4B is a candidate gene for a QTL of thousand grain weight on chromosome 4B. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:2369-2384. [PMID: 35588016 PMCID: PMC9271121 DOI: 10.1007/s00122-022-04118-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 04/25/2022] [Indexed: 06/14/2023]
Abstract
Glutamine synthetase TaGSr-4B is a candidate gene for a QTL of thousand grain weight on 4B, and the gene marker is ready for wheat breeding. A QTL for thousand grain weight (TGW) in wheat was previously mapped on chromosome 4B in a DH population of Westonia × Kauz. For identifying the candidate genes of the QTL, wheat 90 K SNP array was used to saturate the existing linkage map, and four field trials plus one glasshouse experiment over five locations were conducted to refine the QTL. Three nitrogen levels were applied to two of those field trials, resulting in a TGW phenotype data set from nine environments. A robust TGW QTL cluster including 773 genes was detected in six environments with the highest LOD value of 13.4. Based on differentiate gene expression within the QTL cluster in an RNAseq data of Westonia and Kauz during grain filling, a glutamine synthesis gene (GS: TaGSr-4B) was selected as a potential candidate gene for the QTL. A SNP on the promoter region between Westonia and Kauz was used to develop a cleaved amplified polymorphic marker for TaGSr-4B gene mapping and QTL reanalysing. As results, TGW QTL appeared in seven environments, and in four out of seven environments, the TGW QTL were localized on the TaGSr-4B locus and showed significant contributions to the phenotype. Based on the marker, two allele groups of Westonia and Kauz formed showed significant differences on TGW in eight environments. In agreement with the roles of GS genes on nitrogen and carbon remobilizations, TaGSr-4B is likely the candidate gene of the TGW QTL on 4B and the TaGSr-4B gene marker is ready for wheat breeding.
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Affiliation(s)
- Fan Yang
- Australian-China Joint Centre for Wheat Improvement, Food Futures Institute, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, 4 Shizishan Road, Chengdu, 610066, China
| | - Jingjuan Zhang
- Australian-China Joint Centre for Wheat Improvement, Food Futures Institute, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia.
| | - Yun Zhao
- Australian-China Joint Centre for Wheat Improvement, Food Futures Institute, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia
- College of Agronomy, Qingdao Agriculture University, Qingdao, 266109, China
| | - Qier Liu
- Australian-China Joint Centre for Wheat Improvement, Food Futures Institute, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia
| | - Shahidul Islam
- Australian-China Joint Centre for Wheat Improvement, Food Futures Institute, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia
| | - Wuyun Yang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, 4 Shizishan Road, Chengdu, 610066, China
| | - Wujun Ma
- Australian-China Joint Centre for Wheat Improvement, Food Futures Institute, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia.
- College of Agronomy, Qingdao Agriculture University, Qingdao, 266109, China.
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6
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Zhou T, Wu P, Yue C, Huang J, Zhang Z, Hua Y. Transcriptomic Dissection of Allotetraploid Rapeseed (Brassica napus L.) in Responses to Nitrate and Ammonium Regimes and Functional Analysis of BnaA2.Gln1;4 in Arabidopsis. PLANT & CELL PHYSIOLOGY 2022; 63:755-769. [PMID: 35325216 DOI: 10.1093/pcp/pcac037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 03/22/2022] [Indexed: 06/14/2023]
Abstract
Plant roots acquire nitrogen predominantly as two inorganic forms, nitrate (NO3-) and ammonium (NH4+), to which plants respond differentially. Rapeseed (Brassica napus L.) is an important oil-crop species with very low nitrogen-use efficiency (NUE), the regulatory mechanism of which was elusive due to the vastness and complexity of the rapeseed genome. In this study, a comparative transcriptomic analysis was performed to investigate the differential signatures of nitrogen-starved rapeseed in responses to NO3- and NH4+ treatments and to identify the key genes regulating rapeseed NUE. The two nitrogen sources differentially affected the shoot and root transcriptome profiles, including those of genome-wide nitrogen transporter and transcription factor (TF)-related genes. Differential expression profiling showed that BnaA6.NRT2;1 and BnaA7.AMT1;3 might be the core transporters responsible for efficient NO3- and NH4+ uptake, respectively; the TF genes responsive to inorganic nitrogen, specifically responding to NO3-, and specifically responsive to NH4+ were also identified. The genes which were commonly and most significantly affected by both NO3- and NH4+ treatments were related to glutamine metabolism. Among the glutamine synthetase (GS) family genes, we found BnaA2.Gln1;4, significantly responsive to low-nitrogen conditions and showed higher transcription abundance and GS activity in the leaf veins, flower sepals, root cortex and stele, silique petiole and stem tissues. These characters were significantly different from those of AtGln1;4. The heterologous overexpression of BnaA2.Gln1;4 in Arabidopsis increased plant biomass, NUE, GS activity and total amino acid concentrations under both sufficient- and low-nitrogen conditions. Overall, this study provided novel information about the genes involved in the adaptation to different nitrogen regimes and identified some promising candidate genes for enhancing NUE in rapeseed.
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Affiliation(s)
- Ting Zhou
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, PR China
| | - Pengjia Wu
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, PR China
| | - Caipeng Yue
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, PR China
| | - Jinyong Huang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, PR China
| | - Zhenhua Zhang
- College of Resources and Environmental Sciences, Hunan Agricultural University, Changsha 430128, PR China
| | - Yingpeng Hua
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, PR China
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7
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Lebedev VG, Popova AA, Shestibratov KA. Genetic Engineering and Genome Editing for Improving Nitrogen Use Efficiency in Plants. Cells 2021; 10:cells10123303. [PMID: 34943810 PMCID: PMC8699818 DOI: 10.3390/cells10123303] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/18/2021] [Accepted: 11/23/2021] [Indexed: 12/15/2022] Open
Abstract
Low nitrogen availability is one of the main limiting factors for plant growth and development, and high doses of N fertilizers are necessary to achieve high yields in agriculture. However, most N is not used by plants and pollutes the environment. This situation can be improved by enhancing the nitrogen use efficiency (NUE) in plants. NUE is a complex trait driven by multiple interactions between genetic and environmental factors, and its improvement requires a fundamental understanding of the key steps in plant N metabolism—uptake, assimilation, and remobilization. This review summarizes two decades of research into bioengineering modification of N metabolism to increase the biomass accumulation and yield in crops. The expression of structural and regulatory genes was most often altered using overexpression strategies, although RNAi and genome editing techniques were also used. Particular attention was paid to woody plants, which have great economic importance, play a crucial role in the ecosystems and have fundamental differences from herbaceous species. The review also considers the issue of unintended effects of transgenic plants with modified N metabolism, e.g., early flowering—a research topic which is currently receiving little attention. The future prospects of improving NUE in crops, essential for the development of sustainable agriculture, using various approaches and in the context of global climate change, are discussed.
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Affiliation(s)
- Vadim G. Lebedev
- Forest Biotechnology Group, Branch of the Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 142290 Pushchino, Russia;
- Correspondence:
| | - Anna A. Popova
- Department of Botany and Plant Physiology, Voronezh State University of Forestry and Technologies named after G.F. Morozov, 394087 Voronezh, Russia;
| | - Konstantin A. Shestibratov
- Forest Biotechnology Group, Branch of the Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 142290 Pushchino, Russia;
- Department of Botany and Plant Physiology, Voronezh State University of Forestry and Technologies named after G.F. Morozov, 394087 Voronezh, Russia;
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8
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Molecular Regulatory Networks for Improving Nitrogen Use Efficiency in Rice. Int J Mol Sci 2021; 22:ijms22169040. [PMID: 34445746 PMCID: PMC8396546 DOI: 10.3390/ijms22169040] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/15/2021] [Accepted: 08/17/2021] [Indexed: 11/17/2022] Open
Abstract
Nitrogen is an important factor limiting the growth and yield of rice. However, the excessive application of nitrogen will lead to water eutrophication and economic costs. To create rice varieties with high nitrogen use efficiency (NUE) has always been an arduous task in rice breeding. The processes for improving NUE include nitrogen uptake, nitrogen transport from root to shoot, nitrogen assimilation, and nitrogen redistribution, with each step being indispensable to the improvement of NUE. Here, we summarize the effects of absorption, transport, and metabolism of nitrate, ammonium, and amino acids on NUE, as well as the role of hormones in improving rice NUE. Our discussion provide insight for further research in the future.
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9
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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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10
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Multi-gene metabolic engineering of tomato plants results in increased fruit yield up to 23%. Sci Rep 2020; 10:17219. [PMID: 33057137 PMCID: PMC7560729 DOI: 10.1038/s41598-020-73709-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 08/31/2020] [Indexed: 12/14/2022] Open
Abstract
The capacity to assimilate carbon and nitrogen, to transport the resultant sugars and amino acids to sink tissues, and to convert the incoming sugars and amino acids into storage compounds in the sink tissues, are key determinants of crop yield. Given that all of these processes have the potential to co-limit growth, multiple genetic interventions in source and sink tissues, plus transport processes may be necessary to reach the full yield potential of a crop. We used biolistic combinatorial co-transformation (up to 20 transgenes) for increasing C and N flows with the purpose of increasing tomato fruit yield. We observed an increased fruit yield of up to 23%. To better explore the reconfiguration of metabolic networks in these transformants, we generated a dataset encompassing physiological parameters, gene expression and metabolite profiling on plants grown under glasshouse or polytunnel conditions. A Sparse Partial Least Squares regression model was able to explain the combination of genes that contributed to increased fruit yield. This combinatorial study of multiple transgenes targeting primary metabolism thus offers opportunities to probe the genetic basis of metabolic and phenotypic variation, providing insight into the difficulties in choosing the correct combination of targets for engineering increased fruit yield.
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11
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Dellero Y. Manipulating Amino Acid Metabolism to Improve Crop Nitrogen Use Efficiency for a Sustainable Agriculture. FRONTIERS IN PLANT SCIENCE 2020; 11:602548. [PMID: 33329673 PMCID: PMC7733991 DOI: 10.3389/fpls.2020.602548] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 11/03/2020] [Indexed: 05/06/2023]
Abstract
In a context of a growing worldwide food demand coupled to the need to develop a sustainable agriculture, it is crucial to improve crop nitrogen use efficiency (NUE) while reducing field N inputs. Classical genetic approaches based on natural allelic variations existing within crops have led to the discovery of quantitative trait loci controlling NUE under low nitrogen conditions; however, the identification of candidate genes from mapping studies is still challenging. Amino acid metabolism is the cornerstone of plant N management, which involves N uptake, assimilation, and remobilization efficiencies, and it is finely regulated during acclimation to low N conditions and other abiotic stresses. Over the last two decades, biotechnological engineering of amino acid metabolism has led to promising results for the improvement of crop NUE, and more recently under low N conditions. This review summarizes current work carried out in crops and provides perspectives on the identification of new candidate genes and future strategies for crop improvement.
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12
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Schneider A, Godin C, Boudon F, Demotes-Mainard S, Sakr S, Bertheloot J. Light Regulation of Axillary Bud Outgrowth Along Plant Axes: An Overview of the Roles of Sugars and Hormones. FRONTIERS IN PLANT SCIENCE 2019; 10:1296. [PMID: 31681386 PMCID: PMC6813921 DOI: 10.3389/fpls.2019.01296] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 09/18/2019] [Indexed: 05/06/2023]
Abstract
Apical dominance, the process by which the growing apical zone of the shoot inhibits bud outgrowth, involves an intricate network of several signals in the shoot. Auxin originating from plant apical region inhibits bud outgrowth indirectly. This inhibition is in particular mediated by cytokinins and strigolactones, which move from the stem to the bud and that respectively stimulate and repress bud outgrowth. The action of this hormonal network is itself modulated by sugar levels as competition for sugars, caused by the growing apical sugar sink, may deprive buds from sugars and prevents bud outgrowth partly by their signaling role. In this review, we analyze recent findings on the interaction between light, in terms of quantity and quality, and apical dominance regulation. Depending on growth conditions, light may trigger different pathways of the apical dominance regulatory network. Studies pinpoint to the key role of shoot-located cytokinin synthesis for light intensity and abscisic acid synthesis in the bud for R:FR in the regulation of bud outgrowth by light. Our analysis provides three major research lines to get a more comprehensive understanding of light effects on bud outgrowth. This would undoubtedly benefit from the use of computer modeling associated with experimental observations to deal with a regulatory system that involves several interacting signals, feedbacks, and quantitative effects.
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Affiliation(s)
- Anne Schneider
- IRHS, INRA, Agrocampus-Ouest, Université d’Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - Christophe Godin
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, INRIA, Lyon, France
| | | | | | - Soulaiman Sakr
- IRHS, INRA, Agrocampus-Ouest, Université d’Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - Jessica Bertheloot
- IRHS, INRA, Agrocampus-Ouest, Université d’Angers, SFR 4207 QuaSaV, Beaucouzé, France
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Zuluaga DL, Sonnante G. The Use of Nitrogen and Its Regulation in Cereals: Structural Genes, Transcription Factors, and the Role of miRNAs. PLANTS 2019; 8:plants8080294. [PMID: 31434274 PMCID: PMC6724420 DOI: 10.3390/plants8080294] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 08/15/2019] [Accepted: 08/16/2019] [Indexed: 01/31/2023]
Abstract
Cereals and, especially, rice, maize, and wheat, are essential commodities, on which human nutrition is based. Expanding population and food demand have required higher production which has been achieved by increasing fertilization, and especially nitrogen supply to cereal crops. In fact, nitrogen is a crucial nutrient for the plant, but excessive use poses serious environmental and health issues. Therefore, increasing nitrogen use efficiency in cereals is of pivotal importance for sustainable agriculture. The main steps in the use of nitrogen are uptake and transport, reduction and assimilation, and translocation and remobilization. Many studies have been carried out on the genes involved in these phases, and on transcription factors regulating these genes. Lately, increasing attention has been paid to miRNAs responding to abiotic stress, including nutrient deficiency. Many miRNAs have been found to regulate transcription factors acting on the expression of specific genes for nitrogen uptake or remobilization. Recent studies on gene regulatory networks have also demonstrated that miRNAs can interact with several nodes in the network, functioning as key regulators in nitrogen metabolism.
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Affiliation(s)
- Diana L Zuluaga
- Institute of Biosciences and Bioresources, National Research Council, Via Amendola 165/A, 70126 Bari, Italy.
| | - Gabriella Sonnante
- Institute of Biosciences and Bioresources, National Research Council, Via Amendola 165/A, 70126 Bari, Italy.
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Gao Y, de Bang TC, Schjoerring JK. Cisgenic overexpression of cytosolic glutamine synthetase improves nitrogen utilization efficiency in barley and prevents grain protein decline under elevated CO 2. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:1209-1221. [PMID: 30525274 PMCID: PMC6576097 DOI: 10.1111/pbi.13046] [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: 08/29/2018] [Revised: 10/23/2018] [Accepted: 11/09/2018] [Indexed: 05/23/2023]
Abstract
Cytosolic glutamine synthetase (GS1) plays a central role in nitrogen (N) metabolism. The importance of GS1 in N remobilization during reproductive growth has been reported in cereal species but attempts to improve N utilization efficiency (NUE) by overexpressing GS1 have yielded inconsistent results. Here, we demonstrate that transformation of barley (Hordeum vulgare L.) plants using a cisgenic strategy to express an extra copy of native HvGS1-1 lead to increased HvGS1.1 expression and GS1 enzyme activity. GS1 overexpressing lines exhibited higher grain yields and NUE than wild-type plants when grown under three different N supplies and two levels of atmospheric CO2 . In contrast with the wild-type, the grain protein concentration in the GS1 overexpressing lines did not decline when plants were exposed to elevated (800-900 μL/L) atmospheric CO2 . We conclude that an increase in GS1 activity obtained through cisgenic overexpression of HvGS1-1 can improve grain yield and NUE in barley. The extra capacity for N assimilation obtained by GS1 overexpression may also provide a means to prevent declining grain protein levels under elevated atmospheric CO2 .
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Affiliation(s)
- Yajie Gao
- Department of Plant and Environmental SciencesFaculty of ScienceCopenhagen UniversityFrederiksbergDenmark
| | - Thomas C. de Bang
- Department of Plant and Environmental SciencesFaculty of ScienceCopenhagen UniversityFrederiksbergDenmark
| | - Jan K. Schjoerring
- Department of Plant and Environmental SciencesFaculty of ScienceCopenhagen UniversityFrederiksbergDenmark
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15
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Barbier FF, Dun EA, Kerr SC, Chabikwa TG, Beveridge CA. An Update on the Signals Controlling Shoot Branching. TRENDS IN PLANT SCIENCE 2019; 24:220-236. [PMID: 30797425 DOI: 10.1016/j.tplants.2018.12.001] [Citation(s) in RCA: 154] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 12/11/2018] [Accepted: 12/20/2018] [Indexed: 05/21/2023]
Abstract
Many new questions on the regulation of shoot branching have been raised in recent years, prompting a review and reassessment of the role of each signal involved. Sugars and their signaling networks have been attributed a major role in the early events of axillary bud outgrowth, whereas cytokinin appears to play a critical role in the modulation of this process in response to the environment. Perception of the recently discovered hormone strigolactone is now quite well understood, while the downstream targets remain largely unknown. Recent literature has highlighted that auxin export from a bud is important for its subsequent growth.
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Affiliation(s)
- Francois F Barbier
- The University of Queensland, School of Biological Sciences, St. Lucia, QLD 4072, Australia
| | - Elizabeth A Dun
- The University of Queensland, School of Biological Sciences, St. Lucia, QLD 4072, Australia; These authors contributed equally to this publication
| | - Stephanie C Kerr
- The University of Queensland, School of Biological Sciences, St. Lucia, QLD 4072, Australia; These authors contributed equally to this publication
| | - Tinashe G Chabikwa
- The University of Queensland, School of Biological Sciences, St. Lucia, QLD 4072, Australia
| | - Christine A Beveridge
- The University of Queensland, School of Biological Sciences, St. Lucia, QLD 4072, Australia.
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16
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Hu M, Zhao X, Liu Q, Hong X, Zhang W, Zhang Y, Sun L, Li H, Tong Y. Transgenic expression of plastidic glutamine synthetase increases nitrogen uptake and yield in wheat. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:1858-1867. [PMID: 29577547 PMCID: PMC6181211 DOI: 10.1111/pbi.12921] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 03/01/2018] [Accepted: 03/04/2018] [Indexed: 05/18/2023]
Abstract
The plastidic glutamine synthetase isoform (GS2) plays a key role in nitrogen (N) assimilation. We introduced TaGS2-2Abpro::TaGS2-2Ab, the favourable allele of TaGS2-2A in the winter wheat (Triticum aestivum) variety Ji5265. Transgenic expression of TaGS2-2Ab significantly increased GS2 abundance and GS activity in leaves. Two consecutive field experiments showed the transgenic lines had higher grain yield, spike number, grain number per spike and 1000-grain weight than did the wild type under both low N and high N conditions. Analysis of N use-related traits showed that transgenic expression of TaGS2-2Ab increased root ability to acquire N, N uptake before and after flowering, remobilization of N to grains and N harvest index. Measurement of chlorophyll content and net photosynthesis rate in flag leaves during grain filling stage revealed that the transgenic lines had prolonged leaf functional duration as compared with the wild type. These results suggest that TaGS2 plays important role in N use, and the favourable allele TaGS2-2Ab is valuable in engineering wheat with improved N use efficiency and grain yield.
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Affiliation(s)
- Mengyun Hu
- Hebei Laboratory of Crop Genetics and BreedingHebei Academy of Agriculture and Forestry SciencesInstitute for Cereal and Oil CropsShijiazhuangChina
| | - Xueqiang Zhao
- State Key Laboratory for Plant Cell and Chromosome EngineeringChinese Academy of SciencesInstitute of Genetics and Developmental BiologyBeijingChina
| | - Qian Liu
- Hebei Laboratory of Crop Genetics and BreedingHebei Academy of Agriculture and Forestry SciencesInstitute for Cereal and Oil CropsShijiazhuangChina
| | - Xia Hong
- State Key Laboratory for Plant Cell and Chromosome EngineeringChinese Academy of SciencesInstitute of Genetics and Developmental BiologyBeijingChina
| | - Wei Zhang
- State Key Laboratory for Plant Cell and Chromosome EngineeringChinese Academy of SciencesInstitute of Genetics and Developmental BiologyBeijingChina
| | - Yingjun Zhang
- Hebei Laboratory of Crop Genetics and BreedingHebei Academy of Agriculture and Forestry SciencesInstitute for Cereal and Oil CropsShijiazhuangChina
| | - Lijing Sun
- Hebei Laboratory of Crop Genetics and BreedingHebei Academy of Agriculture and Forestry SciencesInstitute for Cereal and Oil CropsShijiazhuangChina
| | - Hui Li
- Hebei Laboratory of Crop Genetics and BreedingHebei Academy of Agriculture and Forestry SciencesInstitute for Cereal and Oil CropsShijiazhuangChina
| | - Yiping Tong
- State Key Laboratory for Plant Cell and Chromosome EngineeringChinese Academy of SciencesInstitute of Genetics and Developmental BiologyBeijingChina
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17
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Lebedev VG, Korobova AV, Shendel GV, Kudoyarova GR, Shestibratov KA. Effect of Glutamine Synthetase Gene Overexpression in Birch (Betula pubescens) Plants on Auxin Content and Rooting in vitro. DOKL BIOCHEM BIOPHYS 2018; 480:143-145. [PMID: 30008095 DOI: 10.1134/s1607672918030043] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Indexed: 01/28/2023]
Abstract
The effects of transformation of downy birch (Betula pubescens Ehrh.) with the GS1 gene encoding the cytosolic form of glutamine synthetase on the rooting of plants in vitro was studied. The transgenic plants had an elevated content of glutamine as well as glutamic and aspartic acids and rooted more rapidly than the control plants. Rooting on a medium containing the glutamine synthetase inhibitor phosphinothricin prevented the accumulation of auxin in birch plants carrying the GS1 gene, indicating the involvement of this enzyme in raising the level of auxins in the transgenic plants. The correlation between the increase in the auxin levels in the transgenic plants carrying the glutamine synthetase gene and the increase in the rooting rate is shown for the first time.
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Affiliation(s)
- V G Lebedev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry (Pushchino Branch), Russian Academy of Sciences, Pushchino, Moscow oblast, 142290, Russia.
| | - A V Korobova
- Ufa Institute of Biology, Russian Academy of Sciences, Ufa, 450054, Russia
| | - G V Shendel
- Ufa Institute of Biology, Russian Academy of Sciences, Ufa, 450054, Russia
| | - G R Kudoyarova
- Ufa Institute of Biology, Russian Academy of Sciences, Ufa, 450054, Russia
| | - K A Shestibratov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry (Pushchino Branch), Russian Academy of Sciences, Pushchino, Moscow oblast, 142290, Russia
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James D, Borphukan B, Fartyal D, Ram B, Singh J, Manna M, Sheri V, Panditi V, Yadav R, Achary VMM, Reddy MK. Concurrent Overexpression of OsGS1;1 and OsGS2 Genes in Transgenic Rice ( Oryza sativa L.): Impact on Tolerance to Abiotic Stresses. FRONTIERS IN PLANT SCIENCE 2018; 9:786. [PMID: 29977247 PMCID: PMC6021690 DOI: 10.3389/fpls.2018.00786] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 05/23/2018] [Indexed: 05/18/2023]
Abstract
Glutamine synthetase (GS) is a key enzyme involved in the nitrogen metabolism of higher plants. Abiotic stresses have adverse effects on crop production and pose a serious threat to global food security. GS activity and expression is known to be significantly modulated by various abiotic stresses. However, very few transgenic overexpression studies of GS have studied its impact on abiotic stress tolerance. GS is also the target enzyme of the broad spectrum herbicide Glufosinate (active ingredient: phosphinothricin). In this study, we investigated the effect of concurrent overexpression of the rice cytosolic GS1 (OsGS1;1) and chloroplastic GS2 (OsGS2) genes in transgenic rice on its tolerance to abiotic stresses and the herbicide Glufosinate. Our results demonstrate that the co-overexpression of OsGS1;1 and OsGS2 isoforms in transgenic rice plants enhanced its tolerance to osmotic and salinity stress at the seedling stage. The transgenic lines maintained significantly higher fresh weight, chlorophyll content, and relative water content than wild type (wt) and null segregant (ns) controls, under both osmotic and salinity stress. The OsGS1;1/OsGS2 co-overexpressing transgenic plants accumulated higher levels of proline but showed lower electrolyte leakage and had lower malondialdehyde (MDA) content under the stress treatments. The transgenic lines showed considerably enhanced photosynthetic and agronomic performance under drought and salinity stress imposed during the reproductive stage, as compared to wt and ns control plants. The grain filling rates of the transgenic rice plants under reproductive stage drought stress (64.6 ± 4.7%) and salinity stress (58.2 ± 4.5%) were significantly higher than control plants, thereby leading to higher yields under these abiotic stress conditions. Preliminary analysis also revealed that the transgenic lines had improved tolerance to methyl viologen induced photo-oxidative stress. Taken together, our results demonstrate that the concurrent overexpression of OsGS1;1 and OsGS2 isoforms in rice enhanced physiological tolerance and agronomic performance under adverse abiotic stress conditions, apparently acting through multiple mechanistic routes. The transgenic rice plants also showed limited tolerance to the herbicide Glufosinate. The advantages and limitations of glutamine synthetase overexpression in crop plants, along with future strategies to overcome these limitations for utilization in crop improvement have also been discussed briefly.
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Affiliation(s)
- Donald James
- Crop Improvement Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Bhabesh Borphukan
- Crop Improvement Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Dhirendra Fartyal
- Crop Improvement Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
- Department of Biotechnology, Uttarakhand Technical University, Dehradun, India
| | - Babu Ram
- Crop Improvement Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
- Department of Biotechnology, Uttarakhand Technical University, Dehradun, India
| | - Jitender Singh
- Crop Improvement Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
- National Institute of Plant Genome Research, New Delhi, India
| | - Mrinalini Manna
- Crop Improvement Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Vijay Sheri
- Crop Improvement Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Varakumar Panditi
- Crop Improvement Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Renu Yadav
- Crop Improvement Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - V. Mohan M. Achary
- Crop Improvement Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Mallireddy K. Reddy
- Crop Improvement Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
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Wang YY, Cheng YH, Chen KE, Tsay YF. Nitrate Transport, Signaling, and Use Efficiency. ANNUAL REVIEW OF PLANT BIOLOGY 2018; 69:85-122. [PMID: 29570365 DOI: 10.1146/annurev-arplant-042817-040056] [Citation(s) in RCA: 292] [Impact Index Per Article: 48.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Nitrogen accounts for approximately 60% of the fertilizer consumed each year; thus, it represents one of the major input costs for most nonlegume crops. Nitrate is one of the two major forms of nitrogen that plants acquire from the soil. Mechanistic insights into nitrate transport and signaling have enabled new strategies for enhancing nitrogen utilization efficiency, for lowering input costs for farming, and, more importantly, for alleviating environmental impacts (e.g., eutrophication and production of the greenhouse gas N2O). Over the past decade, significant progress has been made in understanding how nitrate is acquired from the surroundings, how it is efficiently distributed into different plant tissues in response to environmental changes, how nitrate signaling is perceived and transmitted, and how shoot and root nitrogen status is communicated. Several key components of these processes have proven to be novel tools for enhancing nitrate- and nitrogen-use efficiency. In this review, we focus on the roles of NRT1 and NRT2 in nitrate uptake and nitrate allocation among different tissues; we describe the functions of the transceptor NRT1.1, transcription factors, and small signaling peptides in nitrate signaling and tissue communication; and we compile the new strategies for improving nitrogen-use efficiency.
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Affiliation(s)
- Ya-Yun Wang
- Department of Life Science and Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan
| | - Yu-Hsuan Cheng
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan;
- Molecular and Cell Biology Program, Taiwan International Graduate Program, Academia Sinica, Taipei 115, Taiwan
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei 114, Taiwan
| | - Kuo-En Chen
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan;
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei 114, Taiwan
| | - Yi-Fang Tsay
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan;
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