1
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Zhang Y, Fan X, Wang Y, Kong P, Zhao L, Fan X, Zhang Y. OsNAR2.1 induced endogenous nitrogen concentration variation affects transcriptional expression of miRNAs in rice. FRONTIERS IN PLANT SCIENCE 2023; 14:1093676. [PMID: 36909394 PMCID: PMC9998545 DOI: 10.3389/fpls.2023.1093676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 02/13/2023] [Indexed: 06/18/2023]
Abstract
The studies of rice nitrogen concentration on the expression of miRNA so far are mostly limited to the exogenous nitrogen, leaving the effect of endogenous nitrogen largely unexplored. OsNAR2.1 is a high-affinity nitrate transporter partner protein which plays a central role in nitrate absorption and translocation in rice. The expression of OsNAR2.1 could influence the concentration of the endogenous nitrogen in rice. We showed that the expression and production of miRNA in rice can be influenced by manipulating the endogenous nitrogen concentration via OsNAR2.1 transgenic lines. The small RNA content, particularly 24 nucleotides small RNA, expressed differently in two transgenic rice lines (nitrogen efficient line with overexpression of OsNAR2.1 (Ov199), nitrogen-inefficient line with knockdown OsNAR2.1 by RNAi (RNAi)) compared to the wild-type (NP). Comparative hierarchical clustering expression pattern analysis revealed that the expression profiles of mature miRNA in both transgenic lines were different from NP. Several previously unidentified miRNAs were identified to be differentially expressed under different nitrogen concentrations, namely miR1874, miR5150, chr3-36147, chr4-27017 and chr5-21745. In conclusion, our findings suggest that the level of endogenous nitrogen concentration variation by overexpression or knockdown OsNAR2.1 could mediate the expression pattern and intensity of miRNA in rice, which is of high potential to be used in molecular breeding to improve the rice responses towards nitrogen utilization.
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Affiliation(s)
- Yong Zhang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Jiangsu High Quality Rice Research and Development Center, Nanjing Branch of China National Center for Rice Improvement, Nanjing, China
| | - Xiaoru Fan
- School of Chemistry and Life Science, Anshan Normal University, Anshan, China
| | - Yulong Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Pulin Kong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Ling Zhao
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Jiangsu High Quality Rice Research and Development Center, Nanjing Branch of China National Center for Rice Improvement, Nanjing, China
| | - Xiaorong Fan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
- Zhongshan Biological Breeding Laboratory, Nanjing, China
| | - Yadong Zhang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Jiangsu High Quality Rice Research and Development Center, Nanjing Branch of China National Center for Rice Improvement, Nanjing, China
- Zhongshan Biological Breeding Laboratory, Nanjing, China
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2
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Lu Y, Zhang J, Han Z, Han Z, Li S, Zhang J, Ma H, Han Y. Screening of differentially expressed microRNAs and target genes in two potato varieties under nitrogen stress. BMC PLANT BIOLOGY 2022; 22:478. [PMID: 36207676 PMCID: PMC9547441 DOI: 10.1186/s12870-022-03866-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 09/28/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND A reasonable supply of nitrogen (N) fertilizer is essential for obtaining high-quality, high-level, and stable potato yields, and an improvement in the N utilization efficiency can effectively reduce N fertilizer use. It is important to use accurate, straightforward, and efficient transgenic breeding techniques for the identification of genes that can improve nitrogen use efficiency, thus enabling us to achieve the ultimate goal of breeding N-efficient potato varieties. In recent years, some of the mechanisms of miRNAs have been elucidated via the analysis of the correlation between the expression levels of potato miRNA target genes and regulated genes under conditions of stress, but the role of miRNAs in the inhibition/expression of key genes regulating N metabolism under N stress is still unclear. Our study aimed to identify the role played by specific enzymes and miRNAs in the responses of plants to N stress. RESULTS The roots and leaves of the N-efficient potato variety, Yanshu4 ("Y"), and N-inefficient potato variety, Atlantic ("D"), were collected at the seedling and budding stages after they were exposed to different N fertilizer treatments. The miRNAs expressed differentially under the two types of N stress and their corresponding target genes were first predicted using miRNA and degradome analysis. Then, quantitative polymerase chain reaction (qRT-PCR) was performed to verify the expression of differential miRNAs that were closely related to N metabolism. Finally, the shearing relationship between stu-miR396-5p and its target gene StNiR was determined by analyzing luciferase activity levels. The results showed that NiR activity increased significantly with an increase in the applied N levels from the seedling stage to the budding stage, and NiR responded significantly to different N treatments. miRNA sequencing enabled us to predict 48 families with conserved miRNAs that were mainly involved in N metabolism, carbon metabolism, and amino acid biosynthesis. The differences in the expression of the following miRNAs were identified via screening (high expression levels and P < 0.05): stu-miR396-5p, stu-miR408b-3p_R-1, stu-miR3627-3p, stu-miR482a-3p, stu-miR8036-3p, stu-miR482a-5p, stu-miR827-5p, stu-miR156a_L-1, stu-miR827-3p, stu-miR172b-5p, stu-miR6022-p3_7, stu-miR398a-5p, and stu-miR166c-5p_L-3. Degradome analysis showed that most miRNAs had many-to-many relationships with target genes. The main target genes involved in N metabolism were NiR, NiR1, NRT2.5, and NRT2.7. qRT-PCR analysis showed that there were significant differences in the expression levels of stu-miR396-5p, stu-miR8036-3p, and stu-miR482a-3p in the leaves and roots of the Yanshu4 and Atlantic varieties at the seedling and budding stages under conditions that involved no N and excessive N application; the expression of these miRNAs was induced in response to N stress. The correlation between the differential expression of stu-miR396-5p and its corresponding target gene NiR was further verified by determining the luciferase activity level and was found to be strongly negative. CONCLUSION The activity of NiR was significantly positively correlated with N application from the seedling to the budding stage. Differential miRNAs and target genes showed a many-to-many relationship with each other. The expression of stu-miR396-5p, stu-miR482a-3p, and stu-miR8036-3p in the roots and leaves of the Yanshu4 and Atlantic varieties at the seedling and budding stages was notably different under two types of N stress. Under two types of N stress, stu-miR396-5p was down-regulated in Yanshu4 in the seedling-stage and shoot-stage roots, and up-regulated in seedling-stage roots and shoot-stage leaves; stu-miR482a-3p was up-regulated in the seedling and shoot stages. The expression of stu-miR8036-3p was up-regulated in the leaves and roots at the seedling and budding stages, and down-regulated in roots under both types of N stress. The gene expressing the key enzyme involved in N metabolism, StNiR, and the stu-miR396-5p luciferase assay reporter gene had a strong regulatory relationship with each other. This study provides candidate miRNAs related to nitrogen metabolism and highlights that differential miRNAs play a key role in nitrogen stress in potato, providing insights for future research on miRNAs and their target genes in nitrogen metabolic pathways and breeding nitrogen-efficient potatoes.
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Affiliation(s)
- Yue Lu
- College of Horticulture Research, Jilin Agricultural University, Changchun City, 130118, People's Republic of China
| | - Jingying Zhang
- College of Horticulture Research, Jilin Agricultural University, Changchun City, 130118, People's Republic of China
- College of Resources and Environment, Jilin Agricultural University, Changchun City, 130118, P.R. China
| | - Zhijun Han
- College of Horticulture Research, Jilin Agricultural University, Changchun City, 130118, People's Republic of China
| | - Zhongcai Han
- Jilin Provincial Research Institute of Vegetables and Flowers, Changchun City, 130052, People's Republic of China
| | - Shuang Li
- Teaching and Research Base Management Office, Jilin Agricultural University, Changchun City, 130118, People's Republic of China
| | - Jiayue Zhang
- College of Horticulture Research, Jilin Agricultural University, Changchun City, 130118, People's Republic of China
| | - Haoran Ma
- College of Horticulture Research, Jilin Agricultural University, Changchun City, 130118, People's Republic of China
| | - Yuzhu Han
- College of Horticulture Research, Jilin Agricultural University, Changchun City, 130118, People's Republic of China.
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3
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Zinta R, Tiwari JK, Buckseth T, Thakur K, Goutam U, Kumar D, Challam C, Bhatia N, Poonia AK, Naik S, Singh RK, Thakur AK, Dalamu D, Luthra SK, Kumar V, Kumar M. Root system architecture for abiotic stress tolerance in potato: Lessons from plants. FRONTIERS IN PLANT SCIENCE 2022; 13:926214. [PMID: 36212284 PMCID: PMC9539750 DOI: 10.3389/fpls.2022.926214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 08/25/2022] [Indexed: 06/16/2023]
Abstract
The root is an important plant organ, which uptakes nutrients and water from the soil, and provides anchorage for the plant. Abiotic stresses like heat, drought, nutrients, salinity, and cold are the major problems of potato cultivation. Substantial research advances have been achieved in cereals and model plants on root system architecture (RSA), and so root ideotype (e.g., maize) have been developed for efficient nutrient capture to enhance nutrient use efficiency along with genes regulating root architecture in plants. However, limited work is available on potatoes, with a few illustrations on root morphology in drought and nitrogen stress. The role of root architecture in potatoes has been investigated to some extent under heat, drought, and nitrogen stresses. Hence, this mini-review aims to update knowledge and prospects of strengthening RSA research by applying multi-disciplinary physiological, biochemical, and molecular approaches to abiotic stress tolerance to potatoes with lessons learned from model plants, cereals, and other plants.
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Affiliation(s)
- Rasna Zinta
- Indian Council of Agricultural Research (ICAR)-Central Potato Research Institute, Shimla, Himachal Pradesh, India
- Lovely Professional University, Phagwada, Punjab, India
| | - Jagesh Kumar Tiwari
- Indian Council of Agricultural Research (ICAR)-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Tanuja Buckseth
- Indian Council of Agricultural Research (ICAR)-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Kanika Thakur
- Indian Council of Agricultural Research (ICAR)-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Umesh Goutam
- Lovely Professional University, Phagwada, Punjab, India
| | - Devendra Kumar
- Indian Council of Agricultural Research (ICAR)-Central Potato Research Institute, Regional Station, Meerut, India
| | - Clarissa Challam
- Indian Council of Agricultural Research (ICAR)-Central Potato Research Institute, Regional Station, Shillong, India
| | - Nisha Bhatia
- Indian Council of Agricultural Research (ICAR)-Central Potato Research Institute, Shimla, Himachal Pradesh, India
- School of Biotechnology, Shoolini University, Solan, Himachal Pradesh, India
| | - Anuj K. Poonia
- School of Biotechnology, Shoolini University, Solan, Himachal Pradesh, India
| | - Sharmistha Naik
- Indian Council of Agricultural Research (ICAR)-Central Potato Research Institute, Shimla, Himachal Pradesh, India
- Indian Council of Agricultural Research (ICAR)-National Research Centre for Grapes, Pune, Maharashtra, India
| | - Rajesh K. Singh
- Indian Council of Agricultural Research (ICAR)-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Ajay K. Thakur
- Indian Council of Agricultural Research (ICAR)-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Dalamu Dalamu
- Indian Council of Agricultural Research (ICAR)-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Satish K. Luthra
- Indian Council of Agricultural Research (ICAR)-Central Potato Research Institute, Regional Station, Meerut, India
| | - Vinod Kumar
- Indian Council of Agricultural Research (ICAR)-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Manoj Kumar
- Indian Council of Agricultural Research (ICAR)-Central Potato Research Institute, Regional Station, Meerut, India
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4
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Yuan T, Zhu C, Li G, Liu Y, Yang K, Li Z, Song X, Gao Z. An Integrated Regulatory Network of mRNAs, microRNAs, and lncRNAs Involved in Nitrogen Metabolism of Moso Bamboo. Front Genet 2022; 13:854346. [PMID: 35651936 PMCID: PMC9149284 DOI: 10.3389/fgene.2022.854346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 04/14/2022] [Indexed: 11/18/2022] Open
Abstract
Nitrogen is a key macronutrient essential for plant growth and development, and its availability has a strong influence on biological processes. Nitrogen fertilizer has been widely applied in bamboo forests in recent decades; however, the mechanism of nitrogen metabolism in bamboo is not fully elucidated. Here, we characterized the morphological, physiological, and transcriptome changes of moso bamboo in response to different schemes for nitrogen addition to illuminate the regulation mechanism of nitrogen metabolism. The appropriate addition of nitrogen improved the chlorophyll content and Pn (net photosynthetic rate) of leaves, the nitrogen and ammonium contents of the seedling roots, the biomass of the whole seedling, the number of lateral roots, and the activity of enzymes involved in nitrogen metabolism in the roots. Based on the whole transcriptome data of the roots, a total of 8,632 differentially expressed mRNAs (DEGs) were identified under different nitrogen additions, such as 52 nitrate transporter genes, 6 nitrate reductase genes, 2 nitrite reductase genes, 2 glutamine synthase genes, 2 glutamate synthase genes (GOGAT), 3 glutamate dehydrogenase genes, and 431 TFs belonging to 23 families. Meanwhile, 123 differentially expressed miRNAs (DEMs) and 396 differentially expressed lncRNAs (DELs) were characterized as nitrogen responsive, respectively. Furthermore, 94 DEM-DEG pairs and 23 DEL-DEG pairs involved in nitrogen metabolism were identified. Finally, a predicted regulatory network of nitrogen metabolism was initially constructed, which included 17 nitrogen metabolic pathway genes, 15 TFs, 4 miRNAs, and 10 lncRNAs by conjoint analysis of DEGs, DEMs, and DELs and their regulatory relationships, which was supported by RNA-seq data and qPCR results. The lncRNA-miRNA-mRNA network provides new insights into the regulation mechanism of nitrogen metabolism in bamboo, which facilitates further genetic improvement for bamboo to adapt to the fluctuating nitrogen environment.
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Affiliation(s)
- Tingting Yuan
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo and Rattan Science and Technology, Beijing, China.,International Center for Bamboo and Rattan, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, Beijing, China
| | - Chenglei Zhu
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo and Rattan Science and Technology, Beijing, China.,International Center for Bamboo and Rattan, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, Beijing, China
| | - Guangzhu Li
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo and Rattan Science and Technology, Beijing, China.,International Center for Bamboo and Rattan, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, Beijing, China
| | - Yan Liu
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo and Rattan Science and Technology, Beijing, China.,International Center for Bamboo and Rattan, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, Beijing, China
| | - Kebin Yang
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo and Rattan Science and Technology, Beijing, China.,International Center for Bamboo and Rattan, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, Beijing, China
| | - Zhen Li
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo and Rattan Science and Technology, Beijing, China.,International Center for Bamboo and Rattan, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, Beijing, China
| | - Xinzhang Song
- State Key Laboratory of Subtropical Silviculture, Zhejiang A and F University, Hangzhou, China
| | - Zhimin Gao
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo and Rattan Science and Technology, Beijing, China.,International Center for Bamboo and Rattan, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, Beijing, China
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5
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Sagwal V, Sihag P, Singh Y, Mehla S, Kapoor P, Balyan P, Kumar A, Mir RR, Dhankher OP, Kumar U. Development and characterization of nitrogen and phosphorus use efficiency responsive genic and miRNA derived SSR markers in wheat. Heredity (Edinb) 2022; 128:391-401. [PMID: 35132208 PMCID: PMC9177559 DOI: 10.1038/s41437-022-00506-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 01/24/2022] [Accepted: 01/25/2022] [Indexed: 12/21/2022] Open
Abstract
Among all the nutrients, nitrogen (N) and phosphorous (P) are the most limiting factors reducing wheat production and productivity world-wide. These macronutrients are directly applied to soil in the form of fertilizers. However, only 30-40% of these applied fertilizers are utilized by crop plants, while the rest is lost through volatilization, leaching, and surface run off. Therefore, to overcome the deficiency of N and P, it becomes necessary to improve their use efficiency. Marker-assisted selection (MAS) combined with traditional plant breeding approaches is considered best to improve the N and P use efficiency (N/PUE) of wheat varieties. In this study, we developed and evaluated a total of 98 simple sequence repeat (SSR) markers including 66 microRNAs and 32 gene-specific SSRs on a panel of 10 (N and P efficient/deficient) wheat genotypes. Out of these, 35 SSRs were found polymorphic and have been used for the study of genetic diversity and population differentiation. A set of two SSRs, namely miR171a and miR167a were found candidate markers able to discriminate contrasting genotypes for N/PUE, respectively. Therefore, these two markers could be used as functional markers for characterization of wheat germplasm for N and P use efficiency. Target genes of these miRNAs were found to be highly associated with biological processes (24 GO terms) as compared to molecular function and cellular component and shows differential expression under various P starving conditions and abiotic stresses.
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Affiliation(s)
- Vijeta Sagwal
- Department of Molecular Biology, Biotechnology and Bioinformatics, College of Basic Sciences and Humanities, CCS Haryana Agricultural University, Hisar, 125004, India
| | - Pooja Sihag
- Department of Molecular Biology, Biotechnology and Bioinformatics, College of Basic Sciences and Humanities, CCS Haryana Agricultural University, Hisar, 125004, India
| | - Yogita Singh
- Department of Molecular Biology, Biotechnology and Bioinformatics, College of Basic Sciences and Humanities, CCS Haryana Agricultural University, Hisar, 125004, India
| | - Sheetal Mehla
- Department of Molecular Biology, Biotechnology and Bioinformatics, College of Basic Sciences and Humanities, CCS Haryana Agricultural University, Hisar, 125004, India
| | - Prexha Kapoor
- Department of Molecular Biology, Biotechnology and Bioinformatics, College of Basic Sciences and Humanities, CCS Haryana Agricultural University, Hisar, 125004, India
| | - Priyanka Balyan
- Department of Botany, Deva Nagri P.G. College, CCS University, Meerut, 250001, India
| | - Anuj Kumar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Pusa Campus, New Delhi, 110012, India
| | - Reyazul Rouf Mir
- Division of Genetics and Plant Breeding, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-Kashmir), Srinagar, J&K, India
| | - Om Parkash Dhankher
- Stockbridge School of Agriculture, University of Massachusetts, Amherst, MA, 01003, USA
| | - Upendra Kumar
- Department of Molecular Biology, Biotechnology and Bioinformatics, College of Basic Sciences and Humanities, CCS Haryana Agricultural University, Hisar, 125004, India.
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6
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Mondal R, Kumar A, Chattopadhyay SK. Structural property, molecular regulation, and functional diversity of glutamine synthetase in higher plants: a data-mining bioinformatics approach. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:1565-1584. [PMID: 34628690 DOI: 10.1111/tpj.15536] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 09/24/2021] [Accepted: 10/01/2021] [Indexed: 05/26/2023]
Abstract
Glutamine synthetase (GS; E.C.6.3.1.2) is a key enzyme in higher plants with two isozymes, cytosolic GS1 and plastidic GS2, and involves in the assimilation and recycling of NH4+ ions and maintenance of complex traits such as crop nitrogen-use efficiency and yield. Our present understanding of crop nitrogen-use efficiency and its correlation with the functional role of the GS family genes is inadequate, which delays harnessing the benefit of this key enzyme in crop improvement. In this report, we performed a comprehensive investigation on the phylogenetic relationship, structural properties, complex multilevel gene regulation, and expression patterns of the GS genes to enrich present understanding about the enzyme. Our Gene Ontology and protein-protein interactions analysis revealed the functional aspects of GS isozymes in stress mitigation, aging, nucleotide biosynthesis/transport, DNA repair and response to metals. The insight gained here contributes to the future research strategies in developing climate-smart crops for global sustainability.
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Affiliation(s)
- Raju Mondal
- Mulberry Tissue Culture Lab, Central Sericultural Germplasm Resources Centre (CSGRC), Central Silk Board, Ministry of Textile, Govt. of India, Hosur, 635109, India
| | - Amit Kumar
- Host Plant Section, Central Muga Eri Research & Training Institute, Central Silk Board, Ministry of Textile, Govt. of India, Lahdoigarh, Jorhat, Assam, 785700, India
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7
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Pueyo JJ, Quiñones MA, Coba de la Peña T, Fedorova EE, Lucas MM. Nitrogen and Phosphorus Interplay in Lupin Root Nodules and Cluster Roots. FRONTIERS IN PLANT SCIENCE 2021; 12:644218. [PMID: 33747024 PMCID: PMC7966414 DOI: 10.3389/fpls.2021.644218] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 01/25/2021] [Indexed: 05/17/2023]
Abstract
Nitrogen (N) and phosphorus (P) are two major plant nutrients, and their deficiencies often limit plant growth and crop yield. The uptakes of N or P affect each other, and consequently, understanding N-P interactions is fundamental. Their signaling mechanisms have been studied mostly separately, and integrating N-P interactive regulation is becoming the aim of some recent works. Lupins are singular plants, as, under N and P deficiencies, they are capable to develop new organs, the N2-fixing symbiotic nodules, and some species can also transform their root architecture to form cluster roots, hundreds of short rootlets that alter their metabolism to induce a high-affinity P transport system and enhance synthesis and secretion of organic acids, flavonoids, proteases, acid phosphatases, and proton efflux. These modifications lead to mobilization in the soil of, otherwise unavailable, P. White lupin (Lupinus albus) represents a model plant to study cluster roots and for understanding plant acclimation to nutrient deficiency. It tolerates simultaneous P and N deficiencies and also enhances uptake of additional nutrients. Here, we present the structural and functional modifications that occur in conditions of P and N deficiencies and lead to the organogenesis and altered metabolism of nodules and cluster roots. Some known N and P signaling mechanisms include different factors, including phytohormones and miRNAs. The combination of the individual N and P mechanisms uncovers interactive regulation pathways that concur in nodules and cluster roots. L. albus interlinks N and P recycling processes both in the plant itself and in nature.
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Affiliation(s)
- José J. Pueyo
- Institute of Agricultural Sciences, ICA-CSIC, Madrid, Spain
| | | | | | - Elena E. Fedorova
- K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Science, Moscow, Russia
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8
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Metabolomics Intervention Towards Better Understanding of Plant Traits. Cells 2021; 10:cells10020346. [PMID: 33562333 PMCID: PMC7915772 DOI: 10.3390/cells10020346] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 02/06/2023] Open
Abstract
The majority of the most economically important plant and crop species are enriched with the availability of high-quality reference genome sequences forming the basis of gene discovery which control the important biochemical pathways. The transcriptomics and proteomics resources have also been made available for many of these plant species that intensify the understanding at expression levels. However, still we lack integrated studies spanning genomics–transcriptomics–proteomics, connected to metabolomics, the most complicated phase in phenotype expression. Nevertheless, for the past few decades, emphasis has been more on metabolome which plays a crucial role in defining the phenotype (trait) during crop improvement. The emergence of modern high throughput metabolome analyzing platforms have accelerated the discovery of a wide variety of biochemical types of metabolites and new pathways, also helped in improving the understanding of known existing pathways. Pinpointing the causal gene(s) and elucidation of metabolic pathways are very important for development of improved lines with high precision in crop breeding. Along with other-omics sciences, metabolomics studies have helped in characterization and annotation of a new gene(s) function. Hereby, we summarize several areas in the field of crop development where metabolomics studies have made its remarkable impact. We also assess the recent research on metabolomics, together with other omics, contributing toward genetic engineering to target traits and key pathway(s).
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9
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Yan FH, Zhang LP, Cheng F, Yu DM, Hu JY. Accession-specific flowering time variation in response to nitrate fluctuation in Arabidopsis thalian a. PLANT DIVERSITY 2021; 43:78-85. [PMID: 33778228 PMCID: PMC7987567 DOI: 10.1016/j.pld.2020.05.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 05/22/2020] [Accepted: 05/22/2020] [Indexed: 05/03/2023]
Abstract
Flowering time, a key transition point from vegetative to reproductive growth, is regulated by an intrinsic complex of endogenous and exogenous signals including nutrient status. For hundreds of years, nitrogen has been well known to modulate flowering time, but the molecular genetic basis on how plants adapt to ever-changing nitrogen availability remains not fully explored. Here we explore how Arabidopsis natural variation in flowering time responds to nitrate fluctuation. Upon nitrate availability change, we detect accession- and photoperiod-specific flowering responses, which also feature a accession-specific dependency on growth traits. The flowering time variation correlates well with the expression of floral integrators, SOC1 and FT, in an accession-specific manner. We find that gene expression variation of key hub genes in the photoperiod-circadian-clock (GI), aging (SPLs) and autonomous (FLC) pathways associates with the expression change of these integrators, hence flowering time variation. Our results thus shed light on the molecular genetic mechanisms on regulation of accession- and photoperiod-specific flowering time variation in response to nitrate availability.
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Affiliation(s)
- Fei-Hong Yan
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li-Ping Zhang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Fang Cheng
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Dong-Mei Yu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Jin-Yong Hu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- Corresponding author.
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10
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Islam S, Zhang J, Zhao Y, She M, Ma W. Genetic regulation of the traits contributing to wheat nitrogen use efficiency. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 303:110759. [PMID: 33487345 DOI: 10.1016/j.plantsci.2020.110759] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 10/14/2020] [Accepted: 11/11/2020] [Indexed: 05/25/2023]
Abstract
High nitrogen application aimed at increasing crop yield is offset by higher production costs and negative environmental consequences. For wheat, only one third of the applied nitrogen is utilized, which indicates there is scope for increasing Nitrogen Use Efficiency (NUE). However, achieving greater NUE is challenged by the complexity of the trait, which comprises processes associated with nitrogen uptake, transport, reduction, assimilation, translocation and remobilization. Thus, knowledge of the genetic regulation of these processes is critical in increasing NUE. Although primary nitrogen uptake and metabolism-related genes have been well studied, the relative influence of each towards NUE is not fully understood. Recent attention has focused on engineering transcription factors and identification of miRNAs acting on expression of specific genes related to NUE. Knowledge obtained from model species needs to be translated into wheat using recently-released whole genome sequences, and by exploring genetic variations of NUE-related traits in wild relatives and ancient germplasm. Recent findings indicate the genetic basis of NUE is complex. Pyramiding various genes will be the most effective approach to achieve a satisfactory level of NUE in the field.
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Affiliation(s)
- Shahidul Islam
- State Agricultural Biotechnology Center, Murdoch University, Perth, WA, 6150, Australia
| | - Jingjuan Zhang
- State Agricultural Biotechnology Center, Murdoch University, Perth, WA, 6150, Australia
| | - Yun Zhao
- State Agricultural Biotechnology Center, Murdoch University, Perth, WA, 6150, Australia
| | - Maoyun She
- State Agricultural Biotechnology Center, Murdoch University, Perth, WA, 6150, Australia
| | - Wujun Ma
- State Agricultural Biotechnology Center, Murdoch University, Perth, WA, 6150, Australia.
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11
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Yin H, Li B, Wang X, Xi Z. Effect of ammonium and nitrate supplies on nitrogen and sucrose metabolism of Cabernet Sauvignon (Vitis vinifera cv.). JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2020; 100:5239-5250. [PMID: 32520394 DOI: 10.1002/jsfa.10574] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 05/06/2020] [Accepted: 05/30/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND The quality of wine is highly dependent on the quality of berries. Development of berries is influenced by the type and ratio of different nitrogen supplies in the soil. To understand the impact of varying sources and levels of nitrate and ammonium on sucrose and nitrogen metabolism of Vitis vinifera cv. Cabernet Sauvignon, we tested nutrient solutions with four NO3 - -N:NH4 + -N ratios (100:0, 75:25, 50:50, 0:100) through the root system. RESULTS The form and quantity of nitrogen affected berries and leaves with source-sink relationships. Soluble sugar levels were significantly higher in plants treated with mixed nitrogen sources (75:25 and 50:50) compared to single nitrogen sources (100:0 and 0:100). In particular, treating plants with mixed nitrogen source at a 75:25 ratio resulted in 22% higher fructose levels in berries compared to the 50:50 treatment. In addition, mixed nitrogen treatments resulted in significantly higher amino acid levels and protein content. Mixed nitrogen substrates also increased the expression of enzymes involved in both nitrogen and sucrose metabolism. CONCLUSION Plants did not maximize the nitrogen supply when single form nitrogen was provided, and the mixed nitrogen substrates consistently increased the amount of available carbon and nitrogen in the berries and leaves. We found that NO3 - -N:NH4 + -N ratio of 75:25 was the optimum formula for improving nitrogen and sucrose metabolism, and reducing the competition between nitrogen and sucrose. By examining the nutrient utilization of plants cultivated with different nitrogen forms, the present study provides insights into improving cultivation and production practices. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Haining Yin
- College of Enology, Northwest A&F University, Yangling, Shaanxi, China
| | - Bing Li
- College of Enology, Northwest A&F University, Yangling, Shaanxi, China
| | - Xuefei Wang
- College of Enology, Northwest A&F University, Yangling, Shaanxi, China
| | - Zhumei Xi
- College of Enology, Northwest A&F University, Yangling, Shaanxi, China
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12
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Li X, Chen P, Xie Y, Yan Y, Wang L, Dang H, Zhang J, Xu L, Ma F, Guan Q. Apple SERRATE negatively mediates drought resistance by regulating MdMYB88 and MdMYB124 and microRNA biogenesis. HORTICULTURE RESEARCH 2020; 7:98. [PMID: 32637126 PMCID: PMC7326988 DOI: 10.1038/s41438-020-0320-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 04/03/2020] [Accepted: 04/06/2020] [Indexed: 05/14/2023]
Abstract
The function of serrate (SE) in miRNA biogenesis in Arabidopsis is well elucidated, whereas its role in plant drought resistance is largely unknown. In this study, we report that MdSE acts as a negative regulator of apple (Malus × domestica) drought resistance by regulating the expression levels of MdMYB88 and MdMYB124 and miRNAs, including mdm-miR156, mdm-miR166, mdm-miR172, mdm-miR319, and mdm-miR399. MdSE interacts with MdMYB88 and MdMYB124, two positive regulators of apple drought resistance. MdSE decreases the transcript and protein levels of MdMYB88 and MdMYB124, which directly regulate the expression of MdNCED3, a key enzyme in abscisic acid (ABA) biosynthesis. Furthermore, MdSE is enriched in the same region of the MdNECD3 promoter where MdMYB88/MdMYB124 binds. Consistently, MdSE RNAi transgenic plants are more sensitive to ABA-induced stomatal closure, whereas MdSE OE plants are less sensitive. In addition, under drought stress, MdSE is responsible for the biogenesis of mdm-miR399, a negative regulator of drought resistance, and negatively regulates miRNAs, including mdm-miR156, mdm-miR166, mdm-miR172, and mdm-miR319, which are positive regulators of drought resistance. Taken together, by revealing the negative role of MdSE, our results broaden our understanding of the apple drought response and provide a candidate gene for apple drought improvement through molecular breeding.
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Affiliation(s)
- Xuewei Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi PR China
| | - Pengxiang Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi PR China
| | - Yinpeng Xie
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi PR China
| | - Yan Yan
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi PR China
| | - Liping Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi PR China
| | - Huan Dang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi PR China
| | - Jing Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi PR China
| | - Lingfei Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi PR China
| | - Fengwang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi PR China
| | - Qingmei Guan
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi PR China
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Tiwari JK, Buckseth T, Zinta R, Saraswati A, Singh RK, Rawat S, Chakrabarti SK. Genome-wide identification and characterization of microRNAs by small RNA sequencing for low nitrogen stress in potato. PLoS One 2020; 15:e0233076. [PMID: 32428011 PMCID: PMC7237020 DOI: 10.1371/journal.pone.0233076] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 04/28/2020] [Indexed: 11/18/2022] Open
Abstract
Nitrogen is an important nutrient for plant growth and tuber quality of potato. Since potato crop requires high dose of N, improving nitrogen use efficiency (NUE) of plant is an inevitable approach to minimize N fertilization. The aim of this study was to identify and characterize microRNAs (miRNAs) by small RNA sequencing in potato plants grown in aeroponic under two contrasting N (high and low) regimes. A total of 119 conserved miRNAs belonging to 41 miRNAs families, and 1002 putative novel miRNAs were identified. From total, 52 and 54 conserved miRNAs, and 404 and 628 putative novel miRNAs were differentially expressed in roots and shoots, respectively under low N stress. Of total 34,135 predicted targets, the gene ontology (GO) analysis indicated that maximum targets belong to biological process followed by molecular function and cellular component. Eexpression levels of the selected miRNAs and targets were validated by real time-quantitative polymerase chain reaction (RT-qPCR) analysis. Two predicted targets of potential miRNAs (miR397 and miR398) were validated by 5' RLM-RACE (RNA ligase mediated rapid amplification of cDNA ends). In general, predicted targets are associated with stress-related, kinase, transporters and transcription factors such as universal stress protein, heat shock protein, salt-tolerance protein, calmodulin binding protein, serine-threonine protein kinsae, Cdk10/11- cyclin dependent kinase, amino acid transporter, nitrate transporter, sugar transporter, transcription factor, F-box family protein, and zinc finger protein etc. Our study highlights that miR397 and miR398 play crucial role in potato during low N stress management. Moreover, study provides insights to modulate miRNAs and their predicted targets to develop N-use efficient potato using transgenic/genome-editing tools in future.
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Affiliation(s)
- Jagesh Kumar Tiwari
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India
- * E-mail:
| | - Tanuja Buckseth
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Rasna Zinta
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Aastha Saraswati
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Rajesh Kumar Singh
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Shashi Rawat
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Swarup Kumar Chakrabarti
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India
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14
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Luo B, Xu M, Zhao L, Xie P, Chen Y, Harwood W, Xu G, Fan X, Miller AJ. Overexpression of the High-Affinity Nitrate Transporter OsNRT2.3b Driven by Different Promoters in Barley Improves Yield and Nutrient Uptake Balance. Int J Mol Sci 2020; 21:E1320. [PMID: 32075298 PMCID: PMC7072886 DOI: 10.3390/ijms21041320] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/07/2020] [Accepted: 02/13/2020] [Indexed: 11/29/2022] Open
Abstract
Improving nitrogen use efficiency (NUE) is very important for crops throughout the world. Rice mainly utilizes ammonium as an N source, but it also has four NRT2 genes involved in nitrate transport. The OsNRT2.3b transporter is important for maintaining cellular pH under mixed N supplies. Overexpression of this transporter driven by a ubiquitin promoter in rice greatly improved yield and NUE. This strategy for improving the NUE of crops may also be important for other cereals such as wheat and barley, which also face the challenges of nutrient uptake balance. To test this idea, we constructed transgenic barley lines overexpressing OsNRT2.3b. These transgenic barley lines overexpressing the rice transporter exhibited improved growth, yield, and NUE. We demonstrated that NRT2 family members and the partner protein HvNAR2.3 were also up-regulated by nitrate treatment (0.2 mM) in the transgenic lines. This suggests that the expression of OsNRT2.3b and other HvNRT2 family members were all up-regulated in the transgenic barley to increase the efficiency of N uptake and usage. We also compared the ubiquitin (Ubi) and a phloem-specific (RSs1) promoter-driven expression of OsNRT2.3b. The Ubi promoter failed to improve nutrient uptake balance, whereas the RSs1 promoter succeed in increasing the N, P, and Fe uptake balance. The nutrient uptake enhancement did not include Mn and Mg. Surprisingly, we found that the choice of promoter influenced the barley phenotype, not only increasing NUE and grain yield, but also improving nutrient uptake balance.
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Affiliation(s)
- Bingbing Luo
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (B.L.); (M.X.); (L.Z.); (P.X.); (G.X.)
| | - Man Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (B.L.); (M.X.); (L.Z.); (P.X.); (G.X.)
| | - Limei Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (B.L.); (M.X.); (L.Z.); (P.X.); (G.X.)
| | - Peng Xie
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (B.L.); (M.X.); (L.Z.); (P.X.); (G.X.)
| | - Yi Chen
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK; (Y.C.); (W.H.)
| | - Wendy Harwood
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK; (Y.C.); (W.H.)
| | - Guohua Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (B.L.); (M.X.); (L.Z.); (P.X.); (G.X.)
| | - Xiaorong Fan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (B.L.); (M.X.); (L.Z.); (P.X.); (G.X.)
| | - Anthony J. Miller
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK; (Y.C.); (W.H.)
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15
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Song X, Li Y, Cao X, Qi Y. MicroRNAs and Their Regulatory Roles in Plant-Environment Interactions. ANNUAL REVIEW OF PLANT BIOLOGY 2019; 70:489-525. [PMID: 30848930 DOI: 10.1146/annurev-arplant-050718-100334] [Citation(s) in RCA: 366] [Impact Index Per Article: 73.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
MicroRNAs (miRNAs) are 20-24 nucleotide noncoding RNAs abundant in plants and animals. The biogenesis of plant miRNAs involves transcription of miRNA genes, processing of primary miRNA transcripts by DICER-LIKE proteins into mature miRNAs, and loading of mature miRNAs into ARGONAUTE proteins to form miRNA-induced silencing complex (miRISC). By targeting complementary sequences, miRISC negatively regulates gene expression, thereby coordinating plant development and plant-environment interactions. In this review, we present and discuss recent updates on the mechanisms and regulation of miRNA biogenesis, miRISC assembly and actions as well as the regulatory roles of miRNAs in plant developmental plasticity, abiotic/biotic responses, and symbiotic/parasitic interactions. Finally, we suggest future directions for plant miRNA research.
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Affiliation(s)
- Xianwei Song
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China;
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100039, China
| | - Yan Li
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China;
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China;
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100039, China
| | - Yijun Qi
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China;
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
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16
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Nitrogen Supply and Leaf Age Affect the Expression of TaGS1 or TaGS2 Driven by a Constitutive Promoter in Transgenic Tobacco. Genes (Basel) 2018; 9:genes9080406. [PMID: 30103455 PMCID: PMC6115907 DOI: 10.3390/genes9080406] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 08/01/2018] [Accepted: 08/07/2018] [Indexed: 11/26/2022] Open
Abstract
Glutamine synthetase (GS) plays a key role in nitrogen metabolism. Here, two types of tobacco transformants, overexpressing Triticum aestivum GS1 (TaGS1) or GS2 (TaGS2), were analysed. Four independent transformed lines, GS1-TR1, GS1-TR2, GS2-TR1 and GS2-TR2, were used for the nitrogen treatment. Under nitrogen-sufficient conditions, the leaves of GS2-TR showed high accumulation of the TaGS2 transcript, while those of GS1-TR showed a low TaGS1 transcript levels. However, compared with nitrogen-sufficient conditions, the TaGS1 transcript level increased in the leaves under nitrogen starvation, but the TaGS2 transcript level decreased. In addition, the TaGS1 and TaGS2 transcript levels were highest in the middle leaves under nitrogen-sufficient and starvation conditions. These results show that nitrogen supply and leaf age regulate TaGS expression, even when they are driven by a super-promoter. Additionally, in regard to nitrogen metabolism level, the lower leaves of the GS1-TR exhibited lower NH4+ and higher amino acid contents, while the upper leaves exhibited higher amino acid, soluble protein and chlorophyll contents. The leaves of the GS2-TR exhibited lower NH4+ but higher amino acid, soluble protein and chlorophyll contents. Given the role that GS isoforms play in nitrogen metabolism, these data suggest that TaGS1 overexpression may improve nitrogen transport, and that TaGS2 overexpression may improve nitrogen assimilation under nitrogen stress.
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Shin SY, Jeong JS, Lim JY, Kim T, Park JH, Kim JK, Shin C. Transcriptomic analyses of rice (Oryza sativa) genes and non-coding RNAs under nitrogen starvation using multiple omics technologies. BMC Genomics 2018; 19:532. [PMID: 30005603 PMCID: PMC6043990 DOI: 10.1186/s12864-018-4897-1] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Accepted: 06/26/2018] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Nitrogen (N) is a key macronutrient essential for plant growth, and its availability has a strong influence on crop development. The application of synthetic N fertilizers on crops has increased substantially in recent decades; however, the applied N is not fully utilized due to the low N use efficiency of crops. To overcome this limitation, it is important to understand the genome-wide responses and functions of key genes and potential regulatory factors in N metabolism. RESULTS Here, we characterized changes in the rice (Oryza sativa) transcriptome, including genes, newly identified putative long non-coding RNAs (lncRNAs), and microRNAs (miRNAs) and their target mRNAs in response to N starvation using four different transcriptome approaches. Analysis of rice genes involved in N metabolism and/or transport using strand-specific RNA-Seq identified 2588 novel putative lncRNA encoding loci. Analysis of previously published RNA-Seq datasets revealed a group of N starvation-responsive lncRNAs showing differential expression under other abiotic stress conditions. Poly A-primed sequencing (2P-Seq) revealed alternatively polyadenylated isoforms of N starvation-responsive lncRNAs and provided precise 3' end information on the transcript models of these lncRNAs. Analysis of small RNA-Seq data identified N starvation-responsive miRNAs and down-regulation of miR169 family members, causing de-repression of NF-YA, as confirmed by strand-specific RNA-Seq and qRT-PCR. Moreover, we profiled the N starvation-responsive down-regulation of root-specific miRNA, osa-miR444a.4-3p, and Degradome sequencing confirmed MADS25 as a novel target gene. CONCLUSIONS In this study, we used a combination of multiple RNA-Seq analyses to extensively profile the expression of genes, newly identified lncRNAs, and microRNAs in N-starved rice roots and shoots. Data generated in this study provide an in-depth understanding of the regulatory pathways modulated by N starvation-responsive miRNAs. The results of comprehensive, large-scale data analysis provide valuable information on multiple aspects of the rice transcriptome, which may be useful in understanding the responses of rice plants to changes in the N supply status of soil.
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Affiliation(s)
- Sang-Yoon Shin
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826 Republic of Korea
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826 Republic of Korea
| | - Jin Seo Jeong
- Graduate School of International Agricultural Technology and Crop Biotechnology Institute/GreenBio Science & Technology, Seoul National University, Pyeongchang, 25354 Republic of Korea
- Present address: Laboratory of Plant Molecular Biology, Rockefeller University, 1230 York Avenue, New York, NY 10065 USA
| | - Jae Yun Lim
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826 Republic of Korea
| | - Taewook Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826 Republic of Korea
| | - June Hyun Park
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826 Republic of Korea
| | - Ju-Kon Kim
- Graduate School of International Agricultural Technology and Crop Biotechnology Institute/GreenBio Science & Technology, Seoul National University, Pyeongchang, 25354 Republic of Korea
| | - Chanseok Shin
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826 Republic of Korea
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826 Republic of Korea
- Research Institute of Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826 Republic of Korea
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Tiwari JK, Plett D, Garnett T, Chakrabarti SK, Singh RK. Integrated genomics, physiology and breeding approaches for improving nitrogen use efficiency in potato: translating knowledge from other crops. FUNCTIONAL PLANT BIOLOGY : FPB 2018; 45:587-605. [PMID: 32290962 DOI: 10.1071/fp17303] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 12/06/2017] [Indexed: 05/22/2023]
Abstract
Potato plays a key role in global food and nutritional security. Potato is an N fertiliser-responsive crop, producing high tuber yields. However, excessive use of N can result in environmental damage and high production costs, hence improving nitrogen use efficiency (NUE) of potato plants is one of the sustainable options to address these issues and increase yield. Advanced efforts have been undertaken to improve NUE in other plants like Arabidopsis, rice, wheat and maize through molecular and physiological approaches. Conversely, in potato, NUE studies have predominantly focussed on agronomy or soil management, except for a few researchers who have measured gene expression and proteins relevant to N uptake or metabolism. The focus of this review is to adapt knowledge gained from other plants to inform investigation of N metabolism and associated traits in potato with the aim of improving potato NUE using integrated genomics, physiology and breeding methods.
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Affiliation(s)
- Jagesh K Tiwari
- ICAR-Central Potato Research Institute, Shimla - 171001, Himachal Pradesh, India
| | - Darren Plett
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, SA 5064, Australia
| | - Trevor Garnett
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, SA 5064, Australia
| | - Swarup K Chakrabarti
- ICAR-Central Potato Research Institute, Shimla - 171001, Himachal Pradesh, India
| | - Rajesh K Singh
- ICAR-Central Potato Research Institute, Shimla - 171001, Himachal Pradesh, India
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19
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Plett DC, Holtham LR, Okamoto M, Garnett TP. Nitrate uptake and its regulation in relation to improving nitrogen use efficiency in cereals. Semin Cell Dev Biol 2018; 74:97-104. [DOI: 10.1016/j.semcdb.2017.08.027] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Revised: 08/02/2017] [Accepted: 08/09/2017] [Indexed: 12/27/2022]
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Weber K, Burow M. Nitrogen - essential macronutrient and signal controlling flowering time. PHYSIOLOGIA PLANTARUM 2018; 162:251-260. [PMID: 29095491 DOI: 10.1111/ppl.12664] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Revised: 10/10/2017] [Accepted: 10/25/2017] [Indexed: 06/07/2023]
Abstract
Nitrogen, as limiting nutrient for plant growth and crop yield, is a main component of fertilizers and heavily used in modern agriculture. Early reports from over-application of fertilizers in crop production have shown to repress the transition from vegetative to reproductive phase. For the model plant Arabidopsis thaliana, there is evidence that low nitrogen conditions promote early flowering, while high nitrogen as well as nitrogen starvation conditions display the opposite effect. To gain a better understanding of how nitrogen affects the onset of flowering, we reviewed the existing literature for A. thaliana and carried out a meta-analysis on available transcriptomics data, seeking for potential genes and pathways involved in both nitrogen responses and flowering time control. With this strategy, we aimed at identifying potential gateways for integration of nitrogen signaling and potential regulators that might link the regulatory networks controlling nitrogen and flowering in A. thaliana. We found that photoperiodic pathway genes have high potential to be involved in nitrogen-dependent flowering.
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Affiliation(s)
- Konrad Weber
- DynaMo Center, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Meike Burow
- DynaMo Center, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
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Peña PA, Quach T, Sato S, Ge Z, Nersesian N, Dweikat IM, Soundararajan M, Clemente T. Molecular and phenotypic characterization of transgenic wheat and sorghum events expressing the barley alanine aminotransferase. PLANTA 2017; 246:1097-1107. [PMID: 28801748 DOI: 10.1007/s00425-017-2753-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 08/02/2017] [Indexed: 05/03/2023]
Abstract
The expression of a barley alanine aminotransferase gene impacts agronomic outcomes in a C3 crop, wheat. The use of nitrogen-based fertilizers has become one of the major agronomic inputs in crop production systems. Strategies to enhance nitrogen assimilation and flux in planta are being pursued through the introduction of novel genetic alleles. Here an Agrobacterium-mediated approach was employed to introduce the alanine aminotransferase from barley (Hordeum vulgare), HvAlaAT, into wheat (Triticum aestivum) and sorghum (Sorghum bicolor), regulated by either constitutive or root preferred promoter elements. Plants harboring the transgenic HvAlaAT alleles displayed increased alanine aminotransferase (alt) activity. The enhanced alt activity impacted height, tillering and significantly boosted vegetative biomass relative to controls in wheat evaluated under hydroponic conditions, where the phenotypic outcome across these parameters varied relative to time of year study was conducted. Constitutive expression of HvAlaAT translated to elevation in wheat grain yield under field conditions. In sorghum, expression of HvAlaAT enhanced enzymatic activity, but no changes in phenotypic outcomes were observed. Taken together these results suggest that positive agronomic outcomes can be achieved through enhanced alt activity in a C3 crop, wheat. However, the variability observed across experiments under greenhouse conditions implies the phenotypic outcomes imparted by the HvAlaAT allele in wheat may be impacted by environment.
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Affiliation(s)
- Pamela A Peña
- Department of Agronomy and Horticulture, Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Truyen Quach
- Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Shirley Sato
- Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Zhengxiang Ge
- Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Natalya Nersesian
- Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Ismail M Dweikat
- Department of Agronomy and Horticulture, Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | | | - Tom Clemente
- Department of Agronomy and Horticulture, Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA.
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA.
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22
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Nakano Y, Naito Y, Nakano T, Ohtsuki N, Suzuki K. NSR1/MYR2 is a negative regulator of ASN1 expression and its possible involvement in regulation of nitrogen reutilization in Arabidopsis. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2017; 263:219-225. [PMID: 28818378 DOI: 10.1016/j.plantsci.2017.07.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 05/29/2017] [Accepted: 07/15/2017] [Indexed: 06/07/2023]
Abstract
Nitrogen (N) is a major macronutrient that is essential for plant growth. It is important for us to understand the key genes that are involved in the regulation of N utilization. In this study, we focused on a GARP-type transcription factor known as NSR1/MYR2, which has been reported to be induced under N-deficient conditions. Our results demonstrated that NSR1/MYR2 has a transcriptional repression activity and is specifically expressed in vascular tissues, especially in phloem throughout the plant under daily light-dark cycle regulation. The overexpression of NSR1/MYR2 delays nutrient starvation- and dark-triggered senescence in the mature leaves of excised whole aerial parts of Arabidopsis plants. Furthermore, the expression of asparagine synthetase 1 (ASN1), which plays an important role in N remobilization and reallocation, i.e. N reutilization, in Arabidopsis, is negatively regulated by NSR1/MYR2, since the expressions of NSR1/MYR2 and ASN1 were reciprocally regulated during the light-dark cycle and ASN1 expression was down-regulated in overexpressors of NSR1/MYR2 and up-regulated in T-DNA insertion mutants of NSR1/MYR2. Therefore, the present results suggest that NSR1/MYR2 plays a role in N reutilization as a negative regulator through controlling ASN1 expression.
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Affiliation(s)
- Yoshimi Nakano
- National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki 305-8566, Japan
| | - Yuki Naito
- National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki 305-8566, Japan
| | - Toshitsugu Nakano
- National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki 305-8566, Japan
| | - Namie Ohtsuki
- National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki 305-8566, Japan
| | - Kaoru Suzuki
- National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki 305-8566, Japan.
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23
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Zuluaga DL, De Paola D, Janni M, Curci PL, Sonnante G. Durum wheat miRNAs in response to nitrogen starvation at the grain filling stage. PLoS One 2017; 12:e0183253. [PMID: 28813501 PMCID: PMC5558935 DOI: 10.1371/journal.pone.0183253] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 08/01/2017] [Indexed: 11/24/2022] Open
Abstract
Durum wheat highly depends on nitrogen for seed development and yield, and the obtainment of varieties with a better nitrogen use efficiency is crucial to reduce production costs and environmental pollution. In this study, sequencing of two small RNA libraries obtained from tissues of Ciccio and Svevo cultivars grown under nitrogen starvation conditions produced 84 novel, and 161 conserved miRNAs. Of these, 7 novel and 13 known miRNAs were newly identified in this work. Quantitative PCR analysis of selected miRNAs highlighted that the expression levels of some of them depends on the tissue and on the cultivar, Svevo being the most responsive to nitrogen starvation. A number of target genes were predicted to be involved in nitrogen metabolism. An inverse correlation for the qPCR expression data of miRNA/target pairs miR399b/PHO2, miR393c/AFB2, ttu-novel-61/CCAAT-TF was observed in specific tissues or cultivar. Especially, ttu-novel-61 was down-regulated and its target CCAAT-TF up-regulated in almost all tissues both in Svevo and in Ciccio. Moreover, CCAAT-TF was confirmed to be cleaved by ttu-novel-61 at the expected site. The discovery of miRNAs involved in the response to nitrogen stress represents an important step towards functional analyses, with the final aim to design strategies for improving nitrogen use efficiency in durum wheat.
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Affiliation(s)
- Diana L. Zuluaga
- Institute of Biosciences and Bioresources, National Research Council, Bari, Italy
| | - Domenico De Paola
- Institute of Biosciences and Bioresources, National Research Council, Bari, Italy
| | - Michela Janni
- Institute for Electronics and Magnetism, National Research Council (CNR), Parma, Italy
| | - Pasquale Luca Curci
- Institute of Biosciences and Bioresources, National Research Council, Bari, Italy
| | - Gabriella Sonnante
- Institute of Biosciences and Bioresources, National Research Council, Bari, Italy
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24
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Chu X, Yang L, Wang S, Liu J, Yang H. Physiological and metabolic profiles of common reed provide insights into plant adaptation to low nitrogen conditions. BIOCHEM SYST ECOL 2017. [DOI: 10.1016/j.bse.2017.04.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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25
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Noman A, Aqeel M. miRNA-based heavy metal homeostasis and plant growth. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:10068-10082. [PMID: 28229383 DOI: 10.1007/s11356-017-8593-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 02/07/2017] [Indexed: 05/27/2023]
Abstract
Plants have been naturally gifted with mechanisms to adjust under very high or low nutrient concentrations. Heavy metal toxicity is considered as a major growth and yield-limiting factor for plants. This stress includes essential as well as non-essential metals. MicroRNAs (miRNAs) are known for mediating post-transcriptional regulation by cleaving transcripts or translational inhibition. It is commonly agreed that an extensive understanding of plant miRNAs will significantly help in the induction of tolerance against environmental stresses. With the introduction of the latest technology like next generation sequencing (NGS), a growing figure of miRNAs has been productively recognized in several plants for their diverse roles. These miRNAs are well-known modulators of plant responses to heavy metal (HM) stress. Data regarding metal-responsive miRNAs point out the vital role of plant miRNAs in supplementing metal detoxification by means of transcription factors (TF) or gene regulation. Acting as systemic signals, miRNAs also synchronize different physiological processes for plant responses to metal toxicities. In contrast to practicing techniques, using miRNA is a greatly helpful, pragmatic, and feasible approach. The earlier findings point towards miRNAs as a prospective target to engineer heavy metal tolerance in plants. Therefore, there is a need to augment our knowledge about the orchestrated functions of miRNAs during HM stress. We reviewed the deterministic significance of plant miRNAs in heavy metal tolerance and their role in mediating plant responses to HM toxicities. This review also summarized the topical developments by identification and validation of different metal stress-responsive miRNAs.
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Affiliation(s)
- Ali Noman
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian Province, People's Republic of China.
| | - Muhammad Aqeel
- School of Life Sciences, Lanzhou University, Lanzhou, People's Republic of China
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26
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Beatty PH, Klein MS, Fischer JJ, Lewis IA, Muench DG, Good AG. Understanding Plant Nitrogen Metabolism through Metabolomics and Computational Approaches. PLANTS 2016; 5:plants5040039. [PMID: 27735856 PMCID: PMC5198099 DOI: 10.3390/plants5040039] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 09/21/2016] [Accepted: 09/30/2016] [Indexed: 01/24/2023]
Abstract
A comprehensive understanding of plant metabolism could provide a direct mechanism for improving nitrogen use efficiency (NUE) in crops. One of the major barriers to achieving this outcome is our poor understanding of the complex metabolic networks, physiological factors, and signaling mechanisms that affect NUE in agricultural settings. However, an exciting collection of computational and experimental approaches has begun to elucidate whole-plant nitrogen usage and provides an avenue for connecting nitrogen-related phenotypes to genes. Herein, we describe how metabolomics, computational models of metabolism, and flux balance analysis have been harnessed to advance our understanding of plant nitrogen metabolism. We introduce a model describing the complex flow of nitrogen through crops in a real-world agricultural setting and describe how experimental metabolomics data, such as isotope labeling rates and analyses of nutrient uptake, can be used to refine these models. In summary, the metabolomics/computational approach offers an exciting mechanism for understanding NUE that may ultimately lead to more effective crop management and engineered plants with higher yields.
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Affiliation(s)
- Perrin H Beatty
- Department of Biological Sciences, University of Alberta, 85 Avenue NW, Edmonton, AB T6G 2E9, Canada.
| | - Matthias S Klein
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada.
| | - Jeffrey J Fischer
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada.
| | - Ian A Lewis
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada.
| | - Douglas G Muench
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada.
| | - Allen G Good
- Department of Biological Sciences, University of Alberta, 85 Avenue NW, Edmonton, AB T6G 2E9, Canada.
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27
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Chen M, Wang C, Bao H, Chen H, Wang Y. Genome-wide identification and characterization of novel lncRNAs in Populus under nitrogen deficiency. Mol Genet Genomics 2016; 291:1663-80. [PMID: 27138920 DOI: 10.1007/s00438-016-1210-3] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 04/21/2016] [Indexed: 11/28/2022]
Abstract
Long non-coding RNAs (lncRNAs) have been identified as important regulatory factors of gene expression in eukaryotic species, such as Homo sapiens, Arabidopsis thaliana, and Oryza sativa. However, the systematic identification of potential lncRNAs in trees is comparatively rare. In particular, the characteristics, expression, and regulatory roles of lncRNAs in trees under nutrient stress remain largely unknown. A genome-wide strategy was used in this investigation to identify and characterize novel and low-nitrogen (N)-responsive lncRNAs in Populus tomentosa; 388 unique lncRNA candidates belonging to 380 gene loci were detected and only seven lncRNAs were found to belong to seven conserved non-coding RNA families indicating the majority of P. tomentosa lncRNAs are species-specific. In total, 126 lncRNAs were significantly altered under low-N stress; 8 were repressed, and 118 were induced. Furthermore, 9 and 5 lncRNAs were detected as precursors of 11 known and 14 novel Populus miRNAs, respectively, whereas 4 lncRNAs were targeted by 29 miRNAs belonging to 5 families, including 22 conserved and 7 non-conserved miRNAs. In addition, 15 antisense lncRNAs were identified to be generated from opposite strands of 14 corresponding protein-coding genes. In total, 111 protein-coding genes with regions complementary to 38 lncRNAs were also predicted with some lncRNAs corresponding to multiple genes and vice versa, and their functions were annotated, which further demonstrated the complex regulatory relationship between lncRNAs and protein-coding genes in plants. Moreover, an interaction network among lncRNAs, miRNAs, and mRNAs was investigated. These findings enrich our understanding of lncRNAs in Populus, expand the methods of miRNA identification. Our results present the first global characterization of lncRNAs and their potential target genes in response to nitrogen stress in trees, which provides more information on low-nutrition adaptation mechanisms in woody plants.
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Affiliation(s)
- Min Chen
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, People's Republic of China
| | - Chenlu Wang
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, People's Republic of China
| | - Hai Bao
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, People's Republic of China
| | - Hui Chen
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, People's Republic of China
| | - Yanwei Wang
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, People's Republic of China.
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28
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Shabala S, White RG, Djordjevic MA, Ruan YL, Mathesius U. Root-to-shoot signalling: integration of diverse molecules, pathways and functions. FUNCTIONAL PLANT BIOLOGY : FPB 2016; 43:87-104. [PMID: 32480444 DOI: 10.1071/fp15252] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 10/06/2015] [Indexed: 05/23/2023]
Abstract
Plant adaptive potential is critically dependent upon efficient communication and co-ordination of resource allocation and signalling between above- and below-ground plant parts. Plant roots act as gatekeepers that sense and encode information about soil physical, chemical and biological factors, converting them into a sophisticated network of signals propagated both within the root itself, and also between the root and shoot, to optimise plant performance for a specific set of conditions. In return, plant roots receive and decode reciprocal information coming from the shoot. The communication modes are highly diverse and include a broad range of physical (electric and hydraulic signals, propagating Ca2+ and ROS waves), chemical (assimilates, hormones, peptides and nutrients), and molecular (proteins and RNA) signals. Further, different signalling systems operate at very different timescales. It remains unclear whether some of these signalling systems operate in a priming mode(s), whereas others deliver more specific information about the nature of the signal, or whether they carry the same 'weight'. This review summarises the current knowledge of the above signalling mechanisms, and reveals their hierarchy, and highlights the importance of integration of these signalling components, to enable optimal plant functioning in a dynamic environment.
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Affiliation(s)
- Sergey Shabala
- School of Land and Food, University of Tasmania, Private Bag 54, Hobart, Tas. 7001, Australia
| | | | - Michael A Djordjevic
- Plant Science Division, Research School of Biology, Building 134, Linnaeus Way, The Australian National University, Canberra, ACT 2601, Australia
| | - Yong-Ling Ruan
- School of Environmental and Life Sciences, University of Newcastle, University Drive, Callaghan, NSW 2308, Australia
| | - Ulrike Mathesius
- Plant Science Division, Research School of Biology, Building 134, Linnaeus Way, The Australian National University, Canberra, ACT 2601, Australia
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29
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Shriram V, Kumar V, Devarumath RM, Khare TS, Wani SH. MicroRNAs As Potential Targets for Abiotic Stress Tolerance in Plants. FRONTIERS IN PLANT SCIENCE 2016; 7:817. [PMID: 27379117 PMCID: PMC4906921 DOI: 10.3389/fpls.2016.00817] [Citation(s) in RCA: 179] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 05/25/2016] [Indexed: 05/19/2023]
Abstract
The microRNAs (miRNAs) are small (20-24 nt) sized, non-coding, single stranded riboregulator RNAs abundant in higher organisms. Recent findings have established that plants assign miRNAs as critical post-transcriptional regulators of gene expression in sequence-specific manner to respond to numerous abiotic stresses they face during their growth cycle. These small RNAs regulate gene expression via translational inhibition. Usually, stress induced miRNAs downregulate their target mRNAs, whereas, their downregulation leads to accumulation and function of positive regulators. In the past decade, investigations were mainly aimed to identify plant miRNAs, responsive to individual or multiple environmental factors, profiling their expression patterns and recognizing their roles in stress responses and tolerance. Altered expressions of miRNAs implicated in plant growth and development have been reported in several plant species subjected to abiotic stress conditions such as drought, salinity, extreme temperatures, nutrient deprivation, and heavy metals. These findings indicate that miRNAs may hold the key as potential targets for genetic manipulations to engineer abiotic stress tolerance in crop plants. This review is aimed to provide recent updates on plant miRNAs, their biogenesis and functions, target prediction and identification, computational tools and databases available for plant miRNAs, and their roles in abiotic stress-responses and adaptive mechanisms in major crop plants. Besides, the recent case studies for overexpressing the selected miRNAs for miRNA-mediated enhanced abiotic stress tolerance of transgenic plants have been discussed.
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Affiliation(s)
- Varsha Shriram
- Department of Botany, Prof. Ramkrishna More Arts, Commerce and Science College, Savitribai Phule Pune UniversityPune, India
| | - Vinay Kumar
- Department of Biotechnology, Modern College of Arts, Science and Commerce, Savitribai Phule Pune UniversityPune, India
- *Correspondence: Vinay Kumar
| | - Rachayya M. Devarumath
- Molecular Biology and Genetic Engineering Section, Vasantdada Sugar InstitutePune, India
| | - Tushar S. Khare
- Department of Biotechnology, Modern College of Arts, Science and Commerce, Savitribai Phule Pune UniversityPune, India
| | - Shabir H. Wani
- Division of Genetics and Plant Breeding, Faculty of Agriculture WADURA, Sher-e-Kashmir University of Agricultural Sciences and TechnologyKashmir, India
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30
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Srikanth B, Subhakara Rao I, Surekha K, Subrahmanyam D, Voleti SR, Neeraja CN. Enhanced expression of OsSPL14 gene and its association with yield components in rice (Oryza sativa) under low nitrogen conditions. Gene 2015; 576:441-50. [PMID: 26519999 DOI: 10.1016/j.gene.2015.10.062] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 08/24/2015] [Accepted: 10/23/2015] [Indexed: 11/26/2022]
Abstract
Nitrogen use efficiency (NUE) in rice crop is the need of the hour for reduction of nitrous oxide emission resulting from excess nitrogen (N) fertilizer application and also in reduction of cost of cultivation. Ten rice genotypes were grown under low and recommended dose of N application and characterized in terms of parameters related to yield, yield related components and NUE indicators. Wide genetic variability under low N conditions was observed with significant variation for 15 yield related parameters in interactions of genotypes and treatment. Limitation of N has led to the decrease of all yield and yield related parameters, but for grain filling % and 1000 grain weight. Two genotypes, Rasi and Varadhan have shown minimum differences between low and recommended N conditions. Correlation analysis of various yield components showed the importance of the secondary branches for the total grains under low N. Expression analysis of OsSPL14 (LOC_Os08g39890) gene reported to be associated with increased panicle branching and higher grain yield through real time PCR in leaf and three stages of panicle has shown differential temporal expression and its association with yield and yield related components across the genotypes. The expression of OsSPL14 at panicle stage 3, has shown correlation (P<0.05) with N% in grain. Since OsSPL14 is a functional transcription activator, its association of expression in leaf and three panicle stages with yield components as observed in the present study suggests the role of nitrogen metabolism related genes in plant growth and development and its conversion into yield components in rice.
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Affiliation(s)
- B Srikanth
- ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad 500030, India
| | - I Subhakara Rao
- ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad 500030, India
| | - K Surekha
- ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad 500030, India
| | - D Subrahmanyam
- ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad 500030, India
| | - S R Voleti
- ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad 500030, India
| | - C N Neeraja
- ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad 500030, India.
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31
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Dash M, Yordanov YS, Georgieva T, Kumari S, Wei H, Busov V. A systems biology approach identifies new regulators of poplar root development under low nitrogen. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 84:335-46. [PMID: 26315649 DOI: 10.1111/tpj.13002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 08/14/2015] [Accepted: 08/20/2015] [Indexed: 05/02/2023]
Abstract
In Populus, low nitrogen (LN) elicits rapid and vigorous lateral root (LR) proliferation, which is closely mirrored by corresponding transcriptomic changes. Using transcriptomic data, we built a genetic network encompassing a large proportion of the differentially regulated transcriptome. The network is organized in a hierarchical fashion, centered on 11 genes. Transgenic manipulations of only three of the 11 genes had a strong impact on root development under LN. These three genes encoded an F-box protein similar to Hawaiian Skirt (PtaHWS) and two transcription factors (PtaRAP2.11 and PtaNAC1). Up- and downregulation of the three genes caused increased and decreased root proliferation under LN conditions, respectively. The transgenic manipulations had a strong positive effect on growth under greenhouse conditions including increased shoot and root biomass. The three genes appeared to encompass a putative yet-unknown mechanism that underlies root development under LN. Specifically, the genes are predominantly expressed in roots and have a similar temporal response to LN. More importantly, transgenic manipulation for each of the three genes had a highly significant impact on the expression of the other two. The transgenic manipulations appear to also affect the expression of the regulatory miRNA (PtamiRNA164e) of one of the transcription factors (PtaNAC1), albeit in an opposite fashion. Consistent with a putative function of PtaHWS in proteasome degradation, treatment with proteasome inhibitor reversed the expression changes in the transgenic plants. The insights from this study will allow genetic modifications of root architecture for more efficient and dynamic nitrogen foraging in biofuel crops like poplar.
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Affiliation(s)
- Madhumita Dash
- Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931, USA
| | - Yordan S Yordanov
- Department of Biological Sciences, Eastern Illinois University, Charleston, IL, 61920, USA
| | - Tatyana Georgieva
- Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931, USA
| | - Sapna Kumari
- Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931, USA
| | - Hairong Wei
- Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931, USA
| | - Victor Busov
- Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931, USA
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32
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Nguyen GN, Rothstein SJ, Spangenberg G, Kant S. Role of microRNAs involved in plant response to nitrogen and phosphorous limiting conditions. FRONTIERS IN PLANT SCIENCE 2015; 6:629. [PMID: 26322069 PMCID: PMC4534779 DOI: 10.3389/fpls.2015.00629] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 07/30/2015] [Indexed: 05/22/2023]
Abstract
Plant microRNAs (miRNAs) are a class of small non-coding RNAs which target and regulate the expression of genes involved in several growth, development, and metabolism processes. Recent researches have shown involvement of miRNAs in the regulation of uptake and utilization of nitrogen (N) and phosphorus (P) and more importantly for plant adaptation to N and P limitation conditions by modifications in plant growth, phenology, and architecture and production of secondary metabolites. Developing strategies that allow for the higher efficiency of using both N and P fertilizers in crop production is important for economic and environmental benefits. Improved crop varieties with better adaptation to N and P limiting conditions could be a key approach to achieve this effectively. Furthermore, understanding on the interactions between N and P uptake and use and their regulation is important for the maintenance of nutrient homeostasis in plants. This review describes the possible functions of different miRNAs and their cross-talk relevant to the plant adaptive responses to N and P limiting conditions. In addition, a comprehensive understanding of these processes at molecular level and importance of biological adaptation for improved N and P use efficiency is discussed.
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Affiliation(s)
- Giao N. Nguyen
- Biosciences Research, Department of Economic DevelopmentHorsham, VIC, Australia
| | - Steven J. Rothstein
- Department of Molecular and Cellular Biology, College of Biological Science, University of GuelphGuelph, ON, Canada
| | - German Spangenberg
- Biosciences Research, Department of Economic Development, AgriBio, Centre for AgriBioscienceBundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe UniversityBundoora, VIC, Australia
| | - Surya Kant
- Biosciences Research, Department of Economic DevelopmentHorsham, VIC, Australia
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33
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Budak H, Kantar M, Bulut R, Akpinar BA. Stress responsive miRNAs and isomiRs in cereals. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 235:1-13. [PMID: 25900561 DOI: 10.1016/j.plantsci.2015.02.008] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2014] [Revised: 02/12/2015] [Accepted: 02/13/2015] [Indexed: 05/18/2023]
Abstract
Abiotic and biotic stress conditions are vital determinants in the production of cereals, the major caloric source in human nutrition. Small RNAs, miRNAs and isomiRs are central to post-transcriptional regulation of gene expression in a variety of cellular processes including development and stress responses. Several miRNAs have been identified using new technologies and have roles in stress responses in plants, including cereals. The overall knowledge about the cereal miRNA repertoire, as well as an understanding of complex miRNA mediated mechanisms of target regulation in response to stress conditions, is far from complete. Ongoing efforts that add to our understanding of complex miRNA machinery have implications in plant response to stress conditions. Additionally, sequence variants of miRNAs (isomiRNAs or isomiRs), regulation of their expression through dissection of upstream regulatory elements, the role of Processing-bodies (P-bodies) in miRNA exerted gene regulation and yet unveiled organellar plant miRNAs are newly emerging topics, which will contribute to the elucidation of the miRNA machinery and its role in cereal tolerance against abiotic and biotic stresses.
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Affiliation(s)
- Hikmet Budak
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, 34956 Istanbul, Turkey.
| | - Melda Kantar
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, 34956 Istanbul, Turkey
| | - Reyyan Bulut
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, 34956 Istanbul, Turkey
| | - Bala Ani Akpinar
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, 34956 Istanbul, Turkey
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Paul S, Datta SK, Datta K. miRNA regulation of nutrient homeostasis in plants. FRONTIERS IN PLANT SCIENCE 2015; 6:232. [PMID: 25914709 PMCID: PMC4392614 DOI: 10.3389/fpls.2015.00232] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 03/23/2015] [Indexed: 05/02/2023]
Abstract
Small RNAs including micro RNAs (miRNA) play an indispensable role in cell signaling mechanisms. Generally, miRNAs that are 20-24 nucleotides long bind to specific complementary transcripts, attenuating gene expression at the post-transcriptional level or via translational inhibition. In plants, miRNAs have emerged as the principal regulator of various stress responses, including low nutrient availability. It has been reported that miRNAs are vital for maintaining nutrient homeostasis in plants by regulating the expression of transporters that are involved in nutrient uptake and mobilization. The present review highlights the role of various miRNAs in several macro- or micronutrient deficiencies in plants. Understanding the regulation of different transporters by miRNAs will aid in elucidating the underlying molecular signal transduction mechanisms during nutritional stress. Recent findings regarding nutrient related-miRNAs and their gene regulation machinery may delineate a novel platform for improving the nutritional status of cereal grains or crop biofortification programs in the future.
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Affiliation(s)
| | | | - Karabi Datta
- Translational Research Laboratory of Transgenic Rice, Department of Botany, University of CalcuttaKolkata, India
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35
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Qu B, He X, Wang J, Zhao Y, Teng W, Shao A, Zhao X, Ma W, Wang J, Li B, Li Z, Tong Y. A wheat CCAAT box-binding transcription factor increases the grain yield of wheat with less fertilizer input. PLANT PHYSIOLOGY 2015; 167:411-23. [PMID: 25489021 PMCID: PMC4326744 DOI: 10.1104/pp.114.246959] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 12/04/2014] [Indexed: 05/18/2023]
Abstract
Increasing fertilizer consumption has led to low fertilizer use efficiency and environmental problems. Identifying nutrient-efficient genes will facilitate the breeding of crops with improved fertilizer use efficiency. This research performed a genome-wide sequence analysis of the A (NFYA), B (NFYB), and C (NFYC) subunits of Nuclear Factor Y (NF-Y) in wheat (Triticum aestivum) and further investigated their responses to nitrogen and phosphorus availability in wheat seedlings. Sequence mining together with gene cloning identified 18 NFYAs, 34 NFYBs, and 28 NFYCs. The expression of most NFYAs positively responded to low nitrogen and phosphorus availability. In contrast, microRNA169 negatively responded to low nitrogen and phosphorus availability and degraded NFYAs. Overexpressing TaNFYA-B1, a low-nitrogen- and low-phosphorus-inducible NFYA transcript factor on chromosome 6B, significantly increased both nitrogen and phosphorus uptake and grain yield under differing nitrogen and phosphorus supply levels in a field experiment. The increased nitrogen and phosphorus uptake may have resulted from the fact that that overexpressing TaNFYA-B1 stimulated root development and up-regulated the expression of both nitrate and phosphate transporters in roots. Our results suggest that TaNFYA-B1 plays essential roles in root development and in nitrogen and phosphorus usage in wheat. Furthermore, our results provide new knowledge and valuable gene resources that should be useful in efforts to breed crops targeting high yield with less fertilizer input.
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Affiliation(s)
- Baoyuan Qu
- State Key Laboratory for Plant Cell and Chromosome Engineering (B.Q., X.H., Y.Z., W.T., A.S., X.Z., W.M., Ju.W., B.L., Z.L., Y.T.) and National Center for Plant Gene Research (Ji.W.), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xue He
- State Key Laboratory for Plant Cell and Chromosome Engineering (B.Q., X.H., Y.Z., W.T., A.S., X.Z., W.M., Ju.W., B.L., Z.L., Y.T.) and National Center for Plant Gene Research (Ji.W.), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jing Wang
- State Key Laboratory for Plant Cell and Chromosome Engineering (B.Q., X.H., Y.Z., W.T., A.S., X.Z., W.M., Ju.W., B.L., Z.L., Y.T.) and National Center for Plant Gene Research (Ji.W.), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yanyan Zhao
- State Key Laboratory for Plant Cell and Chromosome Engineering (B.Q., X.H., Y.Z., W.T., A.S., X.Z., W.M., Ju.W., B.L., Z.L., Y.T.) and National Center for Plant Gene Research (Ji.W.), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wan Teng
- State Key Laboratory for Plant Cell and Chromosome Engineering (B.Q., X.H., Y.Z., W.T., A.S., X.Z., W.M., Ju.W., B.L., Z.L., Y.T.) and National Center for Plant Gene Research (Ji.W.), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - An Shao
- State Key Laboratory for Plant Cell and Chromosome Engineering (B.Q., X.H., Y.Z., W.T., A.S., X.Z., W.M., Ju.W., B.L., Z.L., Y.T.) and National Center for Plant Gene Research (Ji.W.), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xueqiang Zhao
- State Key Laboratory for Plant Cell and Chromosome Engineering (B.Q., X.H., Y.Z., W.T., A.S., X.Z., W.M., Ju.W., B.L., Z.L., Y.T.) and National Center for Plant Gene Research (Ji.W.), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wenying Ma
- State Key Laboratory for Plant Cell and Chromosome Engineering (B.Q., X.H., Y.Z., W.T., A.S., X.Z., W.M., Ju.W., B.L., Z.L., Y.T.) and National Center for Plant Gene Research (Ji.W.), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Junyi Wang
- State Key Laboratory for Plant Cell and Chromosome Engineering (B.Q., X.H., Y.Z., W.T., A.S., X.Z., W.M., Ju.W., B.L., Z.L., Y.T.) and National Center for Plant Gene Research (Ji.W.), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Bin Li
- State Key Laboratory for Plant Cell and Chromosome Engineering (B.Q., X.H., Y.Z., W.T., A.S., X.Z., W.M., Ju.W., B.L., Z.L., Y.T.) and National Center for Plant Gene Research (Ji.W.), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhensheng Li
- State Key Laboratory for Plant Cell and Chromosome Engineering (B.Q., X.H., Y.Z., W.T., A.S., X.Z., W.M., Ju.W., B.L., Z.L., Y.T.) and National Center for Plant Gene Research (Ji.W.), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yiping Tong
- State Key Laboratory for Plant Cell and Chromosome Engineering (B.Q., X.H., Y.Z., W.T., A.S., X.Z., W.M., Ju.W., B.L., Z.L., Y.T.) and National Center for Plant Gene Research (Ji.W.), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
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36
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Guan M, Møller IS, Schjoerring JK. Two cytosolic glutamine synthetase isoforms play specific roles for seed germination and seed yield structure in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:203-12. [PMID: 25316065 PMCID: PMC4265158 DOI: 10.1093/jxb/eru411] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Nitrogen (N) remobilization from reserves to sinks is essential for seedling establishment and seed production. Cytosolic glutamine synthetase (GS1) is up-regulated during both seed germination and seed filling in plants. However, the specific roles of the individual GS1 isogenes with respect to N remobilization, early seedling vigour, and final seed productivity are not known. In this study, impairment of seed germination and seedling establishment is demonstrated in the single knockout mutant gln1;2, and the double knockout mutant gln1;1:gln1;2. The negative effect of Gln1;2 deficiency was associated with reduced N remobilization from the cotyledons and could be fully alleviated by exogenous N supply. Following reproductive growth, both the single and double Gln1;2-knockout mutants showed decreased seed yield due to fewer siliques, less seeds per silique, and lower dry weight per seed. The gln1;1 single mutant had normal seed yield structure but primary root development during seed germination was reduced in the presence of external N. Gln1;2 promoter-green fluorescent protein constructs showed that Gln1;2 localizes to the vascular cells of roots, petals, and stamens. It is concluded that Gln1;2 plays an important role in N remobilization for both seedling establishment and seed production in Arabidopsis.
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Affiliation(s)
- M Guan
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - I S Møller
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - J K Schjoerring
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
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37
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Kulcheski FR, Côrrea R, Gomes IA, de Lima JC, Margis R. NPK macronutrients and microRNA homeostasis. FRONTIERS IN PLANT SCIENCE 2015; 6:451. [PMID: 26136763 PMCID: PMC4468412 DOI: 10.3389/fpls.2015.00451] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 06/02/2015] [Indexed: 05/02/2023]
Abstract
Macronutrients are essential elements for plant growth and development. In natural, non-cultivated systems, the availability of macronutrients is not a limiting factor of growth, due to fast recycling mechanisms. However, their availability might be an issue in modern agricultural practices, since soil has been frequently over exploited. From a crop management perspective, the nitrogen (N), phosphorus (P), and potassium (K) are three important limiting factors and therefore frequently added as fertilizers. NPK are among the nutrients that have been reported to alter post-embryonic root developmental processes and consequently, impairs crop yield. To cope with nutrients scarcity, plants have evolved several mechanisms involved in metabolic, physiological, and developmental adaptations. In this scenario, microRNAs (miRNAs) have emerged as additional key regulators of nutrients uptake and assimilation. Some studies have demonstrated the intrinsic relation between miRNAs and their targets, and how they can modulate plants to deal with the NPK availability. In this review, we focus on miRNAs and their regulation of targets involved in NPK metabolism. In general, NPK starvation is related with miRNAs that are involved in root-architectural changes and uptake activity modulation. We further show that several miRNAs were discovered to be involved in plant-microbe symbiosis during N and P uptake, and in this way we present a global view of some studies that were conducted in the last years. The integration of current knowledge about miRNA-NPK signaling may help future studies to focus in good candidates genes for the development of important tools for plant nutritional breeding.
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Affiliation(s)
- Franceli R. Kulcheski
- Departamento de Biofísica, Laboratório de Genomas e Populações de Plantas, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto AlegreBrazil
| | - Régis Côrrea
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de JaneiroBrazil
| | - Igor A. Gomes
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de JaneiroBrazil
| | - Júlio C. de Lima
- Laboratório de Genética Molecular, Instituto de Ciências Biológicas, Universidade de Passo Fundo, Passo FundoBrazil
| | - Rogerio Margis
- Departamento de Biofísica, Laboratório de Genomas e Populações de Plantas, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto AlegreBrazil
- *Correspondence: Rogerio Margis, Departamento de Biofísica, Laboratório de Genomas e Populações de Plantas, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves 9500, Setor IV, Prédio 43431, Sala 213, Porto Alegre, RS, CEP, Brazil
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38
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Thomsen HC, Eriksson D, Møller IS, Schjoerring JK. Cytosolic glutamine synthetase: a target for improvement of crop nitrogen use efficiency? TRENDS IN PLANT SCIENCE 2014; 19:656-63. [PMID: 25017701 DOI: 10.1016/j.tplants.2014.06.002] [Citation(s) in RCA: 137] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Revised: 05/30/2014] [Accepted: 06/02/2014] [Indexed: 05/19/2023]
Abstract
Overexpression of the cytosolic enzyme glutamine synthetase 1 (GS1) has been investigated in numerous cases with the goal of improving crop nitrogen use efficiency. However, the outcome has generally been inconsistent. Here, we review possible reasons underlying the lack of success and conclude that GS1 activity may be downregulated via a chain of processes elicited by metabolic imbalances and environmental constraints. We suggest that a pivotal role of GS1 may be related to the maintenance of essential nitrogen (N) flows and internal N sensing during critical stages of plant development. A number of more refined overexpression strategies exploiting gene stacking combined with tissue and cell specific targeting to overcome metabolic bottlenecks are considered along with their potential in relation to new N management strategies.
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Affiliation(s)
- Hanne C Thomsen
- Department of Plant and Environmental Sciences, Plant and Soil Science Section, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Dennis Eriksson
- Department of Plant and Environmental Sciences, Plant and Soil Science Section, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Inge S Møller
- Department of Plant and Environmental Sciences, Plant and Soil Science Section, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Jan K Schjoerring
- Department of Plant and Environmental Sciences, Plant and Soil Science Section, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark.
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39
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Vidal EA, Moyano TC, Canales J, Gutiérrez RA. Nitrogen control of developmental phase transitions in Arabidopsis thaliana. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:5611-8. [PMID: 25129132 DOI: 10.1093/jxb/eru326] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Nitrogen (N) is an essential macronutrient and a key structural component of macromolecules in plants. N nutrients and metabolites can act as signals that impact on many aspects of plant biology. The plant life cycle involves a series of developmental phase transitions that must be tightly coordinated to external and internal cues in order to ensure plant survival and reproduction. N availability is one of the factors controlling phase changes. In this review, we integrate and summarize the known effects of N over different developmental stages in plants. Substantial advances have been made in our understanding of signalling and N-responsive gene regulatory networks. We focus on the molecular mechanisms underlying N regulation of developmental transitions and the role of putative new regulators that might link N availability to pathways controlling Arabidopsis growth and development from seed germination through the plant reproductive transition.
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Affiliation(s)
- Elena A Vidal
- FONDAP Center for Genome Regulation, Millennium Nucleus Center for Plant Functional Genomics, Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Tomás C Moyano
- FONDAP Center for Genome Regulation, Millennium Nucleus Center for Plant Functional Genomics, Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Javier Canales
- FONDAP Center for Genome Regulation, Millennium Nucleus Center for Plant Functional Genomics, Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Rodrigo A Gutiérrez
- FONDAP Center for Genome Regulation, Millennium Nucleus Center for Plant Functional Genomics, Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile
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40
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Simons M, Saha R, Guillard L, Clément G, Armengaud P, Cañas R, Maranas CD, Lea PJ, Hirel B. Nitrogen-use efficiency in maize (Zea mays L.): from 'omics' studies to metabolic modelling. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:5657-71. [PMID: 24863438 DOI: 10.1093/jxb/eru227] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
In this review, we will present the latest developments in systems biology with particular emphasis on improving nitrogen-use efficiency (NUE) in crops such as maize and demonstrating the application of metabolic models. The review highlights the importance of improving NUE in crops and provides an overview of the transcriptome, proteome, and metabolome datasets available, focusing on a comprehensive understanding of nitrogen regulation. 'Omics' data are hard to interpret in the absence of metabolic flux information within genome-scale models. These models, when integrated with 'omics' data, can serve as a basis for generating predictions that focus and guide further experimental studies. By simulating different nitrogen (N) conditions at a pseudo-steady state, the reactions affecting NUE and additional gene regulations can be determined. Such models thus provide a framework for improving our understanding of the metabolic processes underlying the more efficient use of N-based fertilizers.
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Affiliation(s)
- Margaret Simons
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Rajib Saha
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Lenaïg Guillard
- Adaptation des Plantes à leur Environnement, Unité Mixte de Recherche 1318, INRA-Agro-ParisTech, Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique (INRA), Centre de Versailles-Grignon, RD 10, 78026 Versailles cedex, France
| | - Gilles Clément
- Plateau Technique Spécifique de Chimie du Végétal, Institut National de la Recherche Agronomique (INRA), Centre de Versailles-Grignon, Unité Mixte de Recherche 1318, INRA-Agro-ParisTech, Route de St Cyr, F-78026 Versailles Cedex, France
| | - Patrick Armengaud
- Adaptation des Plantes à leur Environnement, Unité Mixte de Recherche 1318, INRA-Agro-ParisTech, Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique (INRA), Centre de Versailles-Grignon, RD 10, 78026 Versailles cedex, France
| | - Rafael Cañas
- Adaptation des Plantes à leur Environnement, Unité Mixte de Recherche 1318, INRA-Agro-ParisTech, Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique (INRA), Centre de Versailles-Grignon, RD 10, 78026 Versailles cedex, France
| | - Costas D Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Peter J Lea
- Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, UK
| | - Bertrand Hirel
- Adaptation des Plantes à leur Environnement, Unité Mixte de Recherche 1318, INRA-Agro-ParisTech, Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique (INRA), Centre de Versailles-Grignon, RD 10, 78026 Versailles cedex, France
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41
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Bloomfield JA, Rose TJ, King GJ. Sustainable harvest: managing plasticity for resilient crops. PLANT BIOTECHNOLOGY JOURNAL 2014; 12:517-33. [PMID: 24891039 PMCID: PMC4207195 DOI: 10.1111/pbi.12198] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Accepted: 04/14/2014] [Indexed: 05/18/2023]
Abstract
Maintaining crop production to feed a growing world population is a major challenge for this period of rapid global climate change. No consistent conceptual or experimental framework for crop plants integrates information at the levels of genome regulation, metabolism, physiology and response to growing environment. An important role for plasticity in plants is assisting in homeostasis in response to variable environmental conditions. Here, we outline how plant plasticity is facilitated by epigenetic processes that modulate chromatin through dynamic changes in DNA methylation, histone variants, small RNAs and transposable elements. We present examples of plant plasticity in the context of epigenetic regulation of developmental phases and transitions and map these onto the key stages of crop establishment, growth, floral initiation, pollination, seed set and maturation of harvestable product. In particular, we consider how feedback loops of environmental signals and plant nutrition affect plant ontogeny. Recent advances in understanding epigenetic processes enable us to take a fresh look at the crosstalk between regulatory systems that confer plasticity in the context of crop development. We propose that these insights into genotype × environment (G × E) interaction should underpin development of new crop management strategies, both in terms of information-led agronomy and in recognizing the role of epigenetic variation in crop breeding.
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Affiliation(s)
- Justin A Bloomfield
- Southern Cross Plant Science, Southern Cross UniversityLismore, NSW, Australia
| | - Terry J Rose
- Southern Cross Plant Science, Southern Cross UniversityLismore, NSW, Australia
| | - Graham J King
- Southern Cross Plant Science, Southern Cross UniversityLismore, NSW, Australia
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