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Pieri A, Beleggia R, Gioia T, Tong H, Di Vittori V, Frascarelli G, Bitocchi E, Nanni L, Bellucci E, Fiorani F, Pecchioni N, Marzario S, De Quattro C, Limongi AR, De Vita P, Rossato M, Schurr U, David JL, Nikoloski Z, Papa R. Transcriptomic response to nitrogen availability reveals signatures of adaptive plasticity during tetraploid wheat domestication. THE PLANT CELL 2024; 36:3809-3823. [PMID: 39056474 PMCID: PMC11371143 DOI: 10.1093/plcell/koae202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 06/18/2024] [Accepted: 07/17/2024] [Indexed: 07/28/2024]
Abstract
The domestication of crops, coupled with agroecosystem development, is associated with major environmental changes and provides an ideal model of phenotypic plasticity. Here, we examined 32 genotypes of three tetraploid wheat (Triticum turgidum L.) subspecies, wild emmer, emmer, and durum wheat, which are representative of the key stages in the domestication of tetraploid wheat. We developed a pipeline that integrates RNA-Seq data and population genomics to assess gene expression plasticity and identify selection signatures under diverse nitrogen availability conditions. Our analysis revealed differing gene expression responses to nitrogen availability across primary (wild emmer to emmer) and secondary (emmer to durum wheat) domestication. Notably, nitrogen triggered the expression of twice as many genes in durum wheat compared to that in emmer and wild emmer. Unique selection signatures were identified at each stage: primary domestication mainly influenced genes related to biotic interactions, whereas secondary domestication affected genes related to amino acid metabolism, in particular lysine. Selection signatures were found in differentially expressed genes (DEGs), notably those associated with nitrogen metabolism, such as the gene encoding glutamate dehydrogenase (GDH). Overall, our study highlights the pivotal role of nitrogen availability in the domestication and adaptive responses of a major food crop, with varying effects across different traits and growth conditions.
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Affiliation(s)
- Alice Pieri
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, via Brecce Bianche, Ancona 60131, Italy
| | - Romina Beleggia
- Council for Agricultural Research and Economics (CREA), Research Centre for Cereal and Industrial Crops (CREA-CI), Foggia 71122, Italy
| | - Tania Gioia
- School of Agricultural, Forestry, Food and Environmental Sciences, University of Basilicata, Potenza 85100, Italy
| | - Hao Tong
- Bioinformatics Department, Institute of Biochemistry and Biology, University of Potsdam, Potsdam 14476, Germany
- Systems Biology and Mathematical Modeling Group, Max Planck Institute of Molecular Plant Physiology, Potsdam 14476, Germany
| | - Valerio Di Vittori
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, via Brecce Bianche, Ancona 60131, Italy
| | - Giulia Frascarelli
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, via Brecce Bianche, Ancona 60131, Italy
| | - Elena Bitocchi
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, via Brecce Bianche, Ancona 60131, Italy
| | - Laura Nanni
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, via Brecce Bianche, Ancona 60131, Italy
| | - Elisa Bellucci
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, via Brecce Bianche, Ancona 60131, Italy
| | - Fabio Fiorani
- Institute of Biosciences and Geosciences (IBG-2): Plant Sciences, Forschungszentrum Julich GmbH, Julich 52428, Germany
| | - Nicola Pecchioni
- Council for Agricultural Research and Economics (CREA), Research Centre for Cereal and Industrial Crops (CREA-CI), Foggia 71122, Italy
| | - Stefania Marzario
- School of Agricultural, Forestry, Food and Environmental Sciences, University of Basilicata, Potenza 85100, Italy
| | - Concetta De Quattro
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, Verona 37134, Italy
| | - Antonina Rita Limongi
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, Verona 37134, Italy
| | - Pasquale De Vita
- Council for Agricultural Research and Economics (CREA), Research Centre for Cereal and Industrial Crops (CREA-CI), Foggia 71122, Italy
| | - Marzia Rossato
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, Verona 37134, Italy
| | - Ulrich Schurr
- Institute of Biosciences and Geosciences (IBG-2): Plant Sciences, Forschungszentrum Julich GmbH, Julich 52428, Germany
| | - Jacques L David
- AGAP, Univ. Montpellier, CIRAD, INRAE, Institut Agro, Montpellier 34060, France
| | - Zoran Nikoloski
- Bioinformatics Department, Institute of Biochemistry and Biology, University of Potsdam, Potsdam 14476, Germany
- Systems Biology and Mathematical Modeling Group, Max Planck Institute of Molecular Plant Physiology, Potsdam 14476, Germany
| | - Roberto Papa
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, via Brecce Bianche, Ancona 60131, Italy
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Wu Q, Xu J, Zhao Y, Wang Y, Zhou L, Ning L, Shabala S, Zhao H. Transcription factor ZmEREB97 regulates nitrate uptake in maize (Zea mays) roots. PLANT PHYSIOLOGY 2024; 196:535-550. [PMID: 38743701 PMCID: PMC11376383 DOI: 10.1093/plphys/kiae277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/28/2024] [Accepted: 04/12/2024] [Indexed: 05/16/2024]
Abstract
Maize (Zea mays L.) has very strong requirements for nitrogen. However, the molecular mechanisms underlying the regulations of nitrogen uptake and translocation in this species are not fully understood. Here, we report that an APETALA2/ETHYLENE RESPONSE FACTOR (AP2/ERF) transcription factor ZmEREB97 functions as an important regulator in the N signaling network in maize. Predominantly expressed and accumulated in main root and lateral root primordia, ZmEREB97 rapidly responded to nitrate treatment. By overlapping the analyses of differentially expressed genes and conducting a DAP-seq assay, we identified 1,446 potential target genes of ZmEREB97. Among these, 764 genes were coregulated in 2 lines of zmereb97 mutants. Loss of function of ZmEREB97 substantially weakened plant growth under both hydroponic and soil conditions. Physiological characterization of zmereb97 mutant plants demonstrated that reduced biomass and grain yield were both associated with reduced nitrate influx, decreased nitrate content, and less N accumulation. We further demonstrated that ZmEREB97 directly targets and regulates the expression of 6 ZmNRT genes by binding to the GCC-box-related sequences in gene promoters. Collectively, these data suggest that ZmEREB97 is a major positive regulator of the nitrate response and that it plays an important role in optimizing nitrate uptake, offering a target for improvement of nitrogen use efficiency in crops.
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Affiliation(s)
- Qi Wu
- Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
- Institute of Crop Germplasm and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Jinyan Xu
- Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
- Institute of Crop Germplasm and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Yingdi Zhao
- Institute of Crop Germplasm and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Yuancong Wang
- Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
- Institute of Crop Germplasm and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Ling Zhou
- Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
- Institute of Crop Germplasm and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Lihua Ning
- Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
- Institute of Crop Germplasm and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Sergey Shabala
- School of Biological Science, University of Western Australia, Crawley, WA 6009, Australia
- Department of Horticulture and International Research Centre for Environmental Membrane Biology, Foshan University, Foshan 528000, China
| | - Han Zhao
- Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
- Institute of Crop Germplasm and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
- Key Laboratory of Germplasm Innovation in Downstream of Huaihe River, Jiangsu Academy of Agricultural Science, Nanjing 210014, China
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Cheraghvareh L, Pourakbar L, Siavash Moghaddam S, Xiao J. The effect of biofertilizers on nickel accumulation, nitrogen metabolism and amino acid profile of corn (Zea mays L.) exposed to nickel stress. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:49498-49513. [PMID: 39078554 DOI: 10.1007/s11356-024-34507-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 07/23/2024] [Indexed: 07/31/2024]
Abstract
The issue of heavy metal pollution such as nickel poses a significant environmental concern, exerting detrimental effects on the growth and viability of plant life. Plants have various mechanisms to effectively manage heavy metal stress, including the ability to modify their amino acid type and content. This adaptive response allows plants to mitigate the detrimental effects caused by excessive heavy metal accumulation. The aim of this study was to investigate the effect of biofertilizers on nickel accumulation, nitrogen metabolism and amino acid profile of corn (Zea mays L.) cv. 'PL438' exposed to Ni stress. After disinfecting and soaking in water for 24 h, corn seeds were primed with bacterial biofertilizers (T2: NPK + FZ), fungal biofertilizers (T3: Arbuscular mycorrhizal fungi (AMF) + Trichoderma (T)), or a combination of them (T4: NPK + FZ + AMF + T) and were cultured by the hydroponic method in completely controlled conditions. Then, they were simultaneously exposed to nickel chloride at various rates (0, 75, or 150 µM) at the three-leaf stage. They were harvested two weeks later and were subjected to the measurement of Ni content, nitrate and nitrite content, nitrate reductase activity, and amino acid profile by high-performance liquid chromatography. The results showed that the application of Ni at higher rates increased Ni, nitrate, and nitrite contents and nitrate reductase activity. The study of Ni accumulation and TF revealed that Ni accumulated in the roots to a greater extent than in the shoots and TF was < 1 in all treatments. The shoot amino acid profile showed that the treatment of Ni+2 increased som amino acids such as aspartic acid, asparagine, serine, histidine, and glycine versus the control, whereas T4 Ni+2 increased aspartic acid, glutamic acid, threonine and arginine. The change in amino acids in Ni-treated plants may play a key role in their adaptation to Ni stress. The findings indicate that biofertilizers played a crucial role in mitigating the negative impacts of Ni on corn plants through alterations in amino acid composition and decreased absorption and translocation of Ni.
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Affiliation(s)
- Leila Cheraghvareh
- Department of Biology, Faculty of Science, Urmia University, Urmia, 5756151818, Iran
| | - Latifeh Pourakbar
- Department of Biology, Faculty of Science, Urmia University, Urmia, 5756151818, Iran.
| | - Sina Siavash Moghaddam
- Department of Plant Production and Genetics, Faculty of Agriculture, Urmia University, Urmia, Iran
| | - Jianbo Xiao
- Department of Analytical Chemistry and Food Science, Faculty of Food Science and Technology, University of Vigo, Vigo, Spain
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Zhang S, Xu L, Zheng Q, Hu J, Jiang D, Dai T, Tian Z. The tetraploid wheat (Triticum dicoccum (Schrank) Schuebl.) improves nitrogen uptake and assimilation adaptation to nitrogen-deficit stress. PLANTA 2024; 259:151. [PMID: 38733553 DOI: 10.1007/s00425-024-04432-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 05/04/2024] [Indexed: 05/13/2024]
Abstract
MAIN CONCLUSION The genetic diversity in tetraploid wheat provides a genetic pool for improving wheat productivity and environmental resilience. The tetraploid wheat had strong N uptake, translocation, and assimilation capacity under N deficit stress, thus alleviating growth inhibition and plant N loss to maintain healthy development and adapt to environments with low N inputs. Tetraploid wheat with a rich genetic variability provides an indispensable genetic pool for improving wheat yield. Mining the physiological mechanisms of tetraploid wheat in response to nitrogen (N) deficit stress is important for low-N-tolerant wheat breeding. In this study, we selected emmer wheat (Kronos, tetraploid), Yangmai 25 (YM25, hexaploid), and Chinese spring (CS, hexaploid) as materials. We investigated the differences in the response of root morphology, leaf and root N accumulation, N uptake, translocation, and assimilation-related enzymes and gene expression in wheat seedlings of different ploidy under N deficit stress through hydroponic experiments. The tetraploid wheat (Kronos) had stronger adaptability to N deficit stress than the hexaploid wheats (YM25, CS). Kronos had better root growth under low N stress, expanding the N uptake area and enhancing N uptake to maintain higher NO3- and soluble protein contents. Kronos exhibited high TaNRT1.1, TaNRT2.1, and TaNRT2.2 expression in roots, which promoted NO3- uptake, and high TaNRT1.5 and TaNRT1.8 expression in roots and leaves enhanced NO3- translocation to the aboveground. NR and GS activity in roots and leaves of Kronos was higher by increasing the expression of TANIA2, TAGS1, and TAGS2, which enhanced the reduction and assimilation of NO3- as well as the re-assimilation of photorespiratory-released NH4+. Overall, Kronos had strong N uptake, translocation, and assimilation capacity under N deficit stress, alleviating growth inhibition and plant N loss and thus maintaining a healthy development. This study reveals the physiological mechanisms of tetraploid wheat that improve nitrogen uptake and assimilation adaptation under low N stress, which will provide indispensable germplasm resources for elite low-N-tolerant wheat improvement and breeding.
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Affiliation(s)
- Siqi Zhang
- Key Laboratory of Crop Physiology Ecology and Production Management of Ministry of Agriculture, Nanjing Agricultural University, No. 1 Weigang, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Libing Xu
- Key Laboratory of Crop Physiology Ecology and Production Management of Ministry of Agriculture, Nanjing Agricultural University, No. 1 Weigang, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Qiaomei Zheng
- Key Laboratory of Crop Physiology Ecology and Production Management of Ministry of Agriculture, Nanjing Agricultural University, No. 1 Weigang, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Jinling Hu
- Key Laboratory of Crop Physiology Ecology and Production Management of Ministry of Agriculture, Nanjing Agricultural University, No. 1 Weigang, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Dong Jiang
- Key Laboratory of Crop Physiology Ecology and Production Management of Ministry of Agriculture, Nanjing Agricultural University, No. 1 Weigang, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Tingbo Dai
- Key Laboratory of Crop Physiology Ecology and Production Management of Ministry of Agriculture, Nanjing Agricultural University, No. 1 Weigang, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Zhongwei Tian
- Key Laboratory of Crop Physiology Ecology and Production Management of Ministry of Agriculture, Nanjing Agricultural University, No. 1 Weigang, Nanjing, 210095, Jiangsu, People's Republic of China.
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Meng HX, Wang YZ, Yao XL, Xie XR, Dong S, Yuan X, Li X, Gao L, Yang G, Chu X, Wang JG. Reactive oxygen species (ROS) modulate nitrogen signaling using temporal transcriptome analysis in foxtail millet. PLANT MOLECULAR BIOLOGY 2024; 114:37. [PMID: 38602592 DOI: 10.1007/s11103-024-01435-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 02/26/2024] [Indexed: 04/12/2024]
Abstract
Reactive oxygen species (ROS) is a chemically reactive chemical substance containing oxygen and a natural by-product of normal oxygen metabolism. Excessive ROS affect the growth process of crops, which will lead to the decrease of yield. Nitrogen, as a critical nutrient element in plants and plays a vital role in plant growth and crop production. Nitrate is the primary nitrogen source available to plants in agricultural soil and various natural environments. However, the molecular mechanism of ROS-nitrate crosstalk is still unclear. In this study, we used the foxtail millet (Setaria italica L.) as the material to figure it out. Here, we show that excessive NaCl inhibits nitrate-promoted plant growth and nitrogen use efficiency (NUE). NaCl induces ROS accumulation in roots, and ROS inhibits nitrate-induced gene expression in a short time. Surprisingly, low concentration ROS slight promotes and high concentration of ROS inhibits foxtail millet growth under long-term H2O2 treatment. These results may open a new perspective for further exploration of ROS-nitrate signaling pathway in plants.
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Affiliation(s)
- Hui-Xin Meng
- College of Agriculture, Shanxi Agricultural University, Taigu, 030801, China
| | - Yu-Ze Wang
- College of Agriculture, Shanxi Agricultural University, Taigu, 030801, China
| | - Xin-Li Yao
- College of Agriculture, Shanxi Agricultural University, Taigu, 030801, China
| | - Xin-Ran Xie
- College of Agriculture, Shanxi Agricultural University, Taigu, 030801, China
| | - Shuqi Dong
- College of Agriculture, Shanxi Agricultural University, Taigu, 030801, China
- State Key Laboratory of Sustainable Dryland Agriculture (in Preparation), Shanxi Agricultural University, Taigu, 030801, China
| | - Xiangyang Yuan
- College of Agriculture, Shanxi Agricultural University, Taigu, 030801, China
- State Key Laboratory of Sustainable Dryland Agriculture (in Preparation), Shanxi Agricultural University, Taigu, 030801, China
| | - Xiaorui Li
- College of Agriculture, Shanxi Agricultural University, Taigu, 030801, China
- State Key Laboratory of Sustainable Dryland Agriculture (in Preparation), Shanxi Agricultural University, Taigu, 030801, China
| | - Lulu Gao
- College of Agriculture, Shanxi Agricultural University, Taigu, 030801, China
| | - Guanghui Yang
- College of Agriculture, Shanxi Agricultural University, Taigu, 030801, China.
| | - Xiaoqian Chu
- College of Agriculture, Shanxi Agricultural University, Taigu, 030801, China.
| | - Jia-Gang Wang
- College of Agriculture, Shanxi Agricultural University, Taigu, 030801, China.
- Hou Ji Laboratory in Shanxi Province, Shanxi Agricultural University, Taigu, 030801, China.
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Zhao Y, Islam S, Alhabbar Z, Zhang J, O'Hara G, Anwar M, Ma W. Current Progress and Future Prospect of Wheat Genetics Research towards an Enhanced Nitrogen Use Efficiency. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091753. [PMID: 37176811 PMCID: PMC10180859 DOI: 10.3390/plants12091753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 01/16/2023] [Accepted: 01/18/2023] [Indexed: 05/15/2023]
Abstract
To improve the yield and quality of wheat is of great importance for food security worldwide. One of the most effective and significant approaches to achieve this goal is to enhance the nitrogen use efficiency (NUE) in wheat. In this review, a comprehensive understanding of the factors involved in the process of the wheat nitrogen uptake, assimilation and remobilization of nitrogen in wheat were introduced. An appropriate definition of NUE is vital prior to its precise evaluation for the following gene identification and breeding process. Apart from grain yield (GY) and grain protein content (GPC), the commonly recognized major indicators of NUE, grain protein deviation (GPD) could also be considered as a potential trait for NUE evaluation. As a complex quantitative trait, NUE is affected by transporter proteins, kinases, transcription factors (TFs) and micro RNAs (miRNAs), which participate in the nitrogen uptake process, as well as key enzymes, circadian regulators, cross-talks between carbon metabolism, which are associated with nitrogen assimilation and remobilization. A series of quantitative genetic loci (QTLs) and linking markers were compiled in the hope to help discover more efficient and useful genetic resources for breeding program. For future NUE improvement, an exploration for other criteria during selection process that incorporates morphological, physiological and biochemical traits is needed. Applying new technologies from phenomics will allow high-throughput NUE phenotyping and accelerate the breeding process. A combination of multi-omics techniques and the previously verified QTLs and molecular markers will facilitate the NUE QTL-mapping and novel gene identification.
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Affiliation(s)
- Yun Zhao
- Food Futures Institute & College of Science, Health, Engineering and Education, Murdoch University, Perth 6150, Australia
- Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Laboratory of Crop Genetics and Breeding of Hebei, Shijiazhuang 050035, China
| | - Shahidul Islam
- Food Futures Institute & College of Science, Health, Engineering and Education, Murdoch University, Perth 6150, Australia
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58108, USA
| | - Zaid Alhabbar
- Department of Field Crops, College of Agriculture and Forestry, University of Mosul, Mosul 41002, Iraq
| | - Jingjuan Zhang
- Food Futures Institute & College of Science, Health, Engineering and Education, Murdoch University, Perth 6150, Australia
| | - Graham O'Hara
- Food Futures Institute & College of Science, Health, Engineering and Education, Murdoch University, Perth 6150, Australia
| | - Masood Anwar
- Food Futures Institute & College of Science, Health, Engineering and Education, Murdoch University, Perth 6150, Australia
| | - Wujun Ma
- Food Futures Institute & College of Science, Health, Engineering and Education, Murdoch University, Perth 6150, Australia
- College of Agronomy, Qingdao Agriculture University, Qingdao 266109, China
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Transcriptome and Metabolome Reveal the Molecular Mechanism of Barley Genotypes Underlying the Response to Low Nitrogen and Resupply. Int J Mol Sci 2023; 24:ijms24054706. [PMID: 36902137 PMCID: PMC10003240 DOI: 10.3390/ijms24054706] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 02/16/2023] [Accepted: 02/27/2023] [Indexed: 03/05/2023] Open
Abstract
Nitrogen is one of the most important mineral elements for plant growth and development. Excessive nitrogen application not only pollutes the environment, but also reduces the quality of crops. However, are few studies on the mechanism of barley tolerance to low nitrogen at both the transcriptome and metabolomics levels. In this study, the nitrogen-efficient genotype (W26) and the nitrogen-sensitive genotype (W20) of barley were treated with low nitrogen (LN) for 3 days and 18 days, then treated with resupplied nitrogen (RN) from 18 to 21 days. Later, the biomass and the nitrogen content were measured, and RNA-seq and metabolites were analyzed. The nitrogen use efficiency (NUE) of W26 and W20 treated with LN for 21 days was estimated by nitrogen content and dry weight, and the values were 87.54% and 61.74%, respectively. It turned out to have a significant difference in the two genotypes under the LN condition. According to the transcriptome analysis, 7926 differentially expressed genes (DEGs) and 7537 DEGs were identified in the leaves of W26 and W20, respectively, and 6579 DEGs and 7128 DEGs were found in the roots of W26 and W20, respectively. After analysis of the metabolites, 458 differentially expressed metabolites (DAMs) and 425 DAMs were found in the leaves of W26 and W20, respectively, and 486 DAMs and 368 DAMs were found in the roots of W26 and W20, respectively. According to the KEGG joint analysis of DEGs and DAMs, it was discovered that glutathione (GSH) metabolism was the pathway of significant enrichment in the leaves of both W26 and W20. In this study, the metabolic pathways of nitrogen metabolism and GSH metabolism of barley under nitrogen were constructed based on the related DAMs and DEGs. In leaves, GSH, amino acids, and amides were the main identified DAMs, while in roots, GSH, amino acids, and phenylpropanes were mainly found DAMs. Finally, some nitrogen-efficient candidate genes and metabolites were selected based on the results of this study. The responses of W26 and W20 to low nitrogen stress were significantly different at the transcriptional and metabolic levels. The candidate genes that have been screened will be verified in future. These data not only provide new insights into how barley responds to LN, but also provide new directions for studying the molecular mechanisms of barley under abiotic stress.
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Li K, Chen L, Shi W, Hu C, Sha Y, Feng G, Wang E, Chen W, Sui X, Mi G. Impacts of maize hybrids with different nitrogen use efficiency on root-associated microbiota based on distinct rhizosphere soil metabolites. Environ Microbiol 2023; 25:473-492. [PMID: 36451600 DOI: 10.1111/1462-2920.16293] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 11/23/2022] [Indexed: 12/05/2022]
Abstract
Plant genotypes shape root-associated microbiota that affect plant nutrient acquisition and productivity. It is unclear how maize hybrids modify root-associated microbiota and their functions and relationship with nitrogen use efficiency (NUE) by regulating rhizosphere soil metabolites. Here, two N-efficient (NE) (ZD958, DMY3) and two N-inefficient (NIE) maize hybrids (YD9953, LY99) were used to investigate this issue under low N (60 kg N ha-1 , LN) and high N (180 kg N ha-1 , HN) field conditions. NE hybrids had higher yield than NIE hybrids under LN but not HN. NE and NIE hybrids recruited only distinct root-associated bacterial microbiota in LN. The bacterial network stability was stronger in NE than NIE hybrids. Compared with NIE hybrids, NE hybrids recruited more bacterial taxa that have been described as plant growth-promoting rhizobacteria (PGPR), and less related to denitrification and N competition; this resulted in low N2 O emission and high rhizosphere NO3 - -N accumulation. NE and NIE hybrids had distinct rhizosphere soil metabolite patterns, and their specific metabolites were closely related to microbiota and specific genera under LN. Our findings reveal the relationships among plant NUE, rhizosphere soil metabolites, root-associated microbiota, and soil nutrient cycling, and this information is informative for breeding NE crops.
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Affiliation(s)
- Keke Li
- Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, China
| | - La Chen
- Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Wenjun Shi
- Key Laboratory of Plant-Soil Interactions, Ministry of Education, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Conghui Hu
- Key Laboratory of Plant-Soil Interactions, Ministry of Education, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Ye Sha
- Key Laboratory of Plant-Soil Interactions, Ministry of Education, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Guozhong Feng
- College of Resources and Environmental Science, Jilin Agricultural University, Changchun, China
- Key Laboratory of Soil Resource Sustainable Utilization for Jilin Province Commodity Grain Bases, Changchun, China
| | - Entao Wang
- Escuela Nacional de Ciencias Biologicas, Instituto Politecnico Nacional, Mexico City, Mexico
| | | | - Xinhua Sui
- Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Guohua Mi
- Key Laboratory of Plant-Soil Interactions, Ministry of Education, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
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9
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Maize Breeding for Low Nitrogen Inputs in Agriculture: Mechanisms Underlying the Tolerance to the Abiotic Stress. STRESSES 2023. [DOI: 10.3390/stresses3010011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Nitrogen (N) is essential for sustaining life on Earth and plays a vital role in plant growth and thus agricultural production. The excessive use of N fertilizers not only harms the economy, but also the environment. In the context of the environmental impacts caused by agriculture, global maize improvement programs aim to develop cultivars with high N-use efficiency (NUE) to reduce the use of N fertilizers. Since N is highly mobile in plants, NUE is related to numerous little-known morphophysiological and molecular mechanisms. In this review paper we present an overview of the morpho-physiological adaptations of shoot and root, molecular mechanisms involved in plant response to low nitrogen environment, and the genetic effects involved in the control of key traits for NUE. Some studies show that the efficiency of cultivars growing under low N is related to deep root architecture, more lateral roots (LR), and sparser branching of LR, resulting in lower metabolic costs. The NUE cultivars also exhibit more efficient photosynthesis, which affects plant growth under suboptimal nitrogen conditions. In this sense, obtaining superior genotypes for NUE can be achieved with the exploitation of heterosis, as non-additive effects are more important in the expression of traits associated with NUE.
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Kasemsap P, Bloom AJ. Breeding for Higher Yields of Wheat and Rice through Modifying Nitrogen Metabolism. PLANTS (BASEL, SWITZERLAND) 2022; 12:85. [PMID: 36616214 PMCID: PMC9823454 DOI: 10.3390/plants12010085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/21/2022] [Accepted: 12/21/2022] [Indexed: 06/17/2023]
Abstract
Wheat and rice produce nutritious grains that provide 32% of the protein in the human diet globally. Here, we examine how genetic modifications to improve assimilation of the inorganic nitrogen forms ammonium and nitrate into protein influence grain yield of these crops. Successful breeding for modified nitrogen metabolism has focused on genes that coordinate nitrogen and carbon metabolism, including those that regulate tillering, heading date, and ammonium assimilation. Gaps in our current understanding include (1) species differences among candidate genes in nitrogen metabolism pathways, (2) the extent to which relative abundance of these nitrogen forms across natural soil environments shape crop responses, and (3) natural variation and genetic architecture of nitrogen-mediated yield improvement. Despite extensive research on the genetics of nitrogen metabolism since the rise of synthetic fertilizers, only a few projects targeting nitrogen pathways have resulted in development of cultivars with higher yields. To continue improving grain yield and quality, breeding strategies need to focus concurrently on both carbon and nitrogen assimilation and consider manipulating genes with smaller effects or that underlie regulatory networks as well as genes directly associated with nitrogen metabolism.
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Affiliation(s)
- Pornpipat Kasemsap
- Department of Plant Sciences, University of California at Davis, Mailstop 3, Davis, CA 95616, USA
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11
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Zhang K, Li S, Xu Y, Zhou Y, Ran S, Zhao H, Huang W, Xu R, Zhong F. Effect of Nickel Ions on the Physiological and Transcriptional Responses to Carbon and Nitrogen Metabolism in Tomato Roots under Low Nitrogen Levels. Int J Mol Sci 2022; 23:ijms231911398. [PMID: 36232700 PMCID: PMC9569439 DOI: 10.3390/ijms231911398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/20/2022] [Accepted: 09/26/2022] [Indexed: 11/16/2022] Open
Abstract
Nickel (Ni) is an essential trace element for plant growth and a component of the plant body that has many different functions in plants. Although it has been confirmed that nickel ions (Ni2+) havea certain regulatory effect on nitrogen (N) metabolism, there are not enough data to prove whether exogenous Ni2+ can increase the carbon (C) and N metabolism in the roots of tomato seedlingsunder low-nitrogen (LN) conditions. Therefore, through the present experiment, we revealed the key mechanism of Ni2+-mediated tomato root tolerance to LN levels. Tomato plants were cultured at two different N levels (7.66 and 0.383 mmol L−1) and two different Ni2+ levels (0 and 0.1 mg L−1 NiSO4 6H2O) under hydroponic conditions. After nine days, we collected roots for physiological, biochemical, and transcriptome sequencing analyses and found that the activities of N assimilation-related enzymes decreased at LN levels. In contrast, Ni2+ significantly increased the activities of N assimilation-related enzymes and increased the contents of nitrate (NO3−), ammonium (NH4+), and total amino acids. Through root transcriptomic analysis, 3738 differentially expressed genes (DEGs) were identified. DEGs related to C and N metabolism were downregulated after LN application. However, after Ni2+ treatment, PK, PDHB, GAPDH, NR, NiR, GS, GOGAT, and other DEGs related to C and N metabolism were significantly upregulated. In conclusion, our results suggest that Ni2+ can regulate the C and N metabolism pathways in tomato roots to alleviate the impact of LN levels.
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Affiliation(s)
- Kun Zhang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shuhao Li
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yang Xu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuqi Zhou
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shengxiang Ran
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Huanhuan Zhao
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | | | - Ru Xu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Fenglin Zhong
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence:
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12
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Grewal SK, Gill RK. Insights into carbon and nitrogen metabolism and antioxidant potential during vegetative phase in quinoa (Chenopodium quinoa Willd.). PROTOPLASMA 2022; 259:1301-1319. [PMID: 35064825 DOI: 10.1007/s00709-022-01736-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 01/06/2022] [Indexed: 06/14/2023]
Abstract
The present investigation was carried out to understand the impact of carbon and nitrogen metabolism in quinoa genotypes IC411824, IC411825, EC507747 and EC507742 during pre-anthesis stage. It was observed that activities of acid invertase, sucrose synthase (cleavage) and sucrose phosphate synthase (SPS) increased up to 75 days after sowing (DAS) and this might be responsible for providing reducing sugars for the development of vegetative parts. Enhanced activities of nitrate reductase, glutamate synthase, glutamine synthetase during vegetative growth of leaves and stem at 90 DAS assist the fixation of ammonia on glutamate molecule to synthesize amino acids at early stages. However, the glutamate dehydrogenase and nitrite reductase play a central role in the re-assimilation of amides from the amino group of asparaginase. As a result, these photosynthetic products will be responsible for providing both the energy and the C-skeletons for ammonium assimilation during amino acid biosynthesis. Leaves and stem of IC411824 and IC411825 had higher total phenol and total flavonoid content. DPPH (2,2-diphenyl-1-picrylhydrazyl) radical scavenging activity was found to be higher in leaves of IC411825 and in stem of IC411824 and IC411825 indicating their capability to act as natural antioxidants.
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Affiliation(s)
- Satvir Kaur Grewal
- Department of Biochemistry, Punjab Agricultural University, Ludhiana, 141004, India.
| | - Ranjit Kaur Gill
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, India
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13
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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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14
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Ayiti OE, Babalola OO. Factors Influencing Soil Nitrification Process and the Effect on Environment and Health. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2022. [DOI: 10.3389/fsufs.2022.821994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
To meet the global demand for food, several factors have been deployed by agriculturists to supply plants with nitrogen. These factors have been observed to influence the soil nitrification process. Understanding the aftermath effect on the environment and health would provoke efficient management. We review literature on these factors, their aftermath effect on the environment and suggest strategies for better management. Synthetic fertilizers and chemical nitrification inhibitors are the most emphasized factors that influence the nitrification process. The process ceases when pH is <5.0. The range of temperature suitable for the proliferation of ammonia oxidizing archaea is within 30 to 37oC while that of ammonia oxidizing bacteria is within 16 to 23oC. Some of the influencing factors excessively speed up the rate of the nitrification process. This leads to excess production of nitrate, accumulation of nitrite as a result of decoupling between nitritation process and nitratation process. The inhibition mechanism of chemical nitrification inhibitors either causes a reduction in the nitrifying micro-organisms or impedes the amoA gene's function. The effects on the environment are soil acidification, global warming, and eutrophication. Some of the health effects attributed to the influence are methemoglobinemia, neurotoxicity, phytotoxicity and cancer. Biomagnification of the chemicals along the food chain is also a major concern. The use of well-researched and scientifically formulated organic fertilizers consisting of microbial inoculum, well-treated organic manure and good soil conditioner are eco-friendly. They are encouraged to be used to efficiently manage the process. Urban agriculture could promote food production, but environmental sustainability should be ensured.
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15
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Yang D, Zhao J, Bi C, Li L, Wang Z. Transcriptome and Proteomics Analysis of Wheat Seedling Roots Reveals That Increasing NH 4 +/NO 3 - Ratio Induced Root Lignification and Reduced Nitrogen Utilization. FRONTIERS IN PLANT SCIENCE 2022; 12:797260. [PMID: 35095967 PMCID: PMC8792948 DOI: 10.3389/fpls.2021.797260] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 12/15/2021] [Indexed: 06/12/2023]
Abstract
Wheat growth and nitrogen (N) uptake gradually decrease in response to high NH4 +/NO3 - ratio. However, the mechanisms underlying the response of wheat seedling roots to changes in NH4 +/NO3 - ratio remain unclear. In this study, we investigated wheat growth, transcriptome, and proteome profiles of roots in response to increasing NH4 +/NO3 - ratios (N a : 100/0; N r1: 75/25, N r2: 50/50, N r3: 25/75, and N n : 0/100). High NH4 +/NO3 - ratio significantly reduced leaf relative chlorophyll content, Fv/Fm, and ΦII values. Both total root length and specific root length decreased with increasing NH4 +/NO3 - ratios. Moreover, the rise in NH4 +/NO3 - ratio significantly promoted O2 - production. Furthermore, transcriptome sequencing and tandem mass tag-based quantitative proteome analyses identified 14,376 differentially expressed genes (DEGs) and 1,819 differentially expressed proteins (DEPs). The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis indicated that glutathione metabolism and phenylpropanoid biosynthesis were the main two shared enriched pathways across ratio comparisons. Upregulated DEGs and DEPs involving glutathione S-transferases may contribute to the prevention of oxidative stress. An increment in the NH4 +/NO3 - ratio induced the expression of genes and proteins involved in lignin biosynthesis, which increased root lignin content. Additionally, phylogenetic tree analysis showed that both A0A3B6NPP6 and A0A3B6LM09 belong to the cinnamyl-alcohol dehydrogenase subfamily. Fifteen downregulated DEGs were identified as high-affinity nitrate transporters or nitrate transporters. Upregulated TraesCS3D02G344800 and TraesCS3A02G350800 were involved in ammonium transport. Downregulated A0A3B6Q9B3 is involved in nitrate transport, whereas A0A3B6PQS3 is a ferredoxin-nitrite reductase. This may explain why an increase in the NH4 +/NO3 - ratio significantly reduced root NO3 --N content but increased NH4 +-N content. Overall, these results demonstrated that increasing the NH4 +/NO3 - ratio at the seedling stage induced the accumulation of reactive oxygen species, which in turn enhanced root glutathione metabolism and lignification, thereby resulting in increased root oxidative tolerance at the cost of reducing nitrate transport and utilization, which reduced leaf photosynthetic capacity and, ultimately, plant biomass accumulation.
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16
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Ravazzolo L, Boutet-Mercey S, Perreau F, Forestan C, Varotto S, Ruperti B, Quaggiotti S. Strigolactones and Auxin Cooperate to Regulate Maize Root Development and Response to Nitrate. PLANT & CELL PHYSIOLOGY 2021; 62:610-623. [PMID: 33508105 DOI: 10.1093/pcp/pcab014] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 01/20/2021] [Indexed: 05/12/2023]
Abstract
In maize, nitrate regulates root development thanks to the coordinated action of many players. In this study, the involvement of strigolactones (SLs) and auxin as putative components of the nitrate regulation of lateral root (LR) was investigated. To this aim, the endogenous SL content of maize root in response to nitrate was assessed by liquid chromatography with tandem mass Spectrometry (LC-MS/MS) and measurements of LR density in the presence of analogues or inhibitors of auxin and SLs were performed. Furthermore, an untargeted RNA-sequencing (RNA-seq)-based approach was used to better characterize the participation of auxin and SLs to the transcriptional signature of maize root response to nitrate. Our results suggested that N deprivation induces zealactone and carlactonoic acid biosynthesis in root, to a higher extent if compared to P-deprived roots. Moreover, data on LR density led to hypothesize that the induction of LR development early occurring upon nitrate supply involves the inhibition of SL biosynthesis, but that the downstream target of SL shutdown, besides auxin, also includes additional unknown players. Furthermore, RNA-seq results provided a set of putative markers for the auxin- or SL-dependent action of nitrate, meanwhile also allowing to identify novel components of the molecular regulation of maize root response to nitrate. Globally, the existence of at least four different pathways was hypothesized: one dependent on auxin, a second one mediated by SLs, a third deriving from the SL-auxin interplay, and a last one attributable to nitrate itself through further downstream signals. Further work will be necessary to better assess the reliability of the model proposed.
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Affiliation(s)
- Laura Ravazzolo
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Viale dell'Università 16, Legnaro 35020, Italy
| | - Stéphanie Boutet-Mercey
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles 78000, France
| | - François Perreau
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles 78000, France
| | - Cristian Forestan
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, Viale Fanin 44, Bologna 40127, Italy
| | - Serena Varotto
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Viale dell'Università 16, Legnaro 35020, Italy
| | - Benedetto Ruperti
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Viale dell'Università 16, Legnaro 35020, Italy
| | - Silvia Quaggiotti
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Viale dell'Università 16, Legnaro 35020, Italy
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17
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Liu Y, Bai L, Sun M, Wang J, Li S, Miao L, Yan Y, He C, Yu X, Li Y. Adaptation of cucumber seedlings to low temperature stress by reducing nitrate to ammonium during it's transportation. BMC PLANT BIOLOGY 2021; 21:189. [PMID: 33874888 PMCID: PMC8056598 DOI: 10.1186/s12870-021-02918-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 03/07/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Low temperature severely depresses the uptake, translocation from the root to the shoot, and metabolism of nitrate and ammonium in thermophilic plants such as cucumber (Cucumis sativus). Plant growth is inhibited accordingly. However, the availability of information on the effects of low temperature on nitrogen transport remains limited. RESULTS Using non-invasive micro-test technology, the net nitrate (NO3-) and ammonium (NH4+) fluxes in the root hair zone and vascular bundles of the primary root, stem, petiole, midrib, lateral vein, and shoot tip of cucumber seedlings under normal temperature (NT; 26 °C) and low temperature (LT; 8 °C) treatment were analyzed. Under LT treatment, the net NO3- flux rate in the root hair zone and vascular bundles of cucumber seedlings decreased, whereas the net NH4+ flux rate in vascular bundles of the midrib, lateral vein, and shoot tip increased. Accordingly, the relative expression of CsNRT1.4a in the petiole and midrib was down-regulated, whereas the expression of CsAMT1.2a-1.2c in the midrib was up-regulated. The results of 15N isotope tracing showed that NO3--N and NH4+-N uptake of the seedlings under LT treatment decreased significantly compared with that under NT treatment, and the concentration and proportion of both NO3--N and NH4+-N distributed in the shoot decreased. Under LT treatment, the actual nitrate reductase activity (NRAact) in the root did not change significantly, whereas NRAact in the stem and petiole increased by 113.2 and 96.2%, respectively. CONCLUSIONS The higher net NH4+ flux rate in leaves and young tissues may reflect the higher NRAact in the stem and petiole, which may result in a higher proportion of NO3- being reduced to NH4+ during the upward transportation of NO3-. The results contribute to an improved understanding of the mechanism of changes in nitrate transportation in plants in response to low-temperature stress.
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Affiliation(s)
- Yumei Liu
- The Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
- College of Agricultural and Biological Engineering, Heze University, Heze, 274000 Shandong China
| | - Longqiang Bai
- College of Horticulture, Shanxi Agricultural University, Taigu, 030801 Shanxi China
| | - Mintao Sun
- The Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Jun Wang
- The Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Shuzhen Li
- College of Life Science, Gannan Normal University, Ganzhou, 341000 Jiangxi China
| | - Li Miao
- The Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Yan Yan
- The Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Chaoxing He
- The Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Xianchang Yu
- The Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Yansu Li
- The Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
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18
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Feng J, Selvam B, Shukla D. How do antiporters exchange substrates across the cell membrane? An atomic-level description of the complete exchange cycle in NarK. Structure 2021; 29:922-933.e3. [PMID: 33836147 DOI: 10.1016/j.str.2021.03.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 01/07/2021] [Accepted: 03/19/2021] [Indexed: 11/19/2022]
Abstract
Major facilitator superfamily (MFS) proteins operate via three different mechanisms: uniport, symport, and antiport. Despite extensive investigations, the molecular understanding of antiporters is less advanced than that of other transporters due to the complex coupling between two substrates and the lack of distinct structures. We employ extensive all-atom molecular dynamics simulations to dissect the complete substrate exchange cycle of the bacterial NO3-/NO2- antiporter, NarK. We show that paired basic residues in the binding site prevent the closure of unbound protein and ensure the exchange of two substrates. Conformational transition occurs only in the presence of substrate, which weakens the electrostatic repulsion and stabilizes the transporter. Furthermore, we propose a state-dependent substrate exchange model, in which the relative spacing between the paired basic residues determines whether NO3- and NO2- bind simultaneously or sequentially. Overall, this work presents a general working model for the antiport mechanism within the MFS.
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Affiliation(s)
- Jiangyan Feng
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Balaji Selvam
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Diwakar Shukla
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; NIH Center for Macromolecular Modeling and Bioinformatics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Center for Digital Agriculture, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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19
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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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20
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Sandhu N, Sethi M, Kumar A, Dang D, Singh J, Chhuneja P. Biochemical and Genetic Approaches Improving Nitrogen Use Efficiency in Cereal Crops: A Review. FRONTIERS IN PLANT SCIENCE 2021; 12:657629. [PMID: 34149755 PMCID: PMC8213353 DOI: 10.3389/fpls.2021.657629] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 04/06/2021] [Indexed: 05/22/2023]
Abstract
Nitrogen is an essential nutrient required in large quantities for the proper growth and development of plants. Nitrogen is the most limiting macronutrient for crop production in most of the world's agricultural areas. The dynamic nature of nitrogen and its tendency to lose soil and environment systems create a unique and challenging environment for its proper management. Exploiting genetic diversity, developing nutrient efficient novel varieties with better agronomy and crop management practices combined with improved crop genetics have been significant factors behind increased crop production. In this review, we highlight the various biochemical, genetic factors and the regulatory mechanisms controlling the plant nitrogen economy necessary for reducing fertilizer cost and improving nitrogen use efficiency while maintaining an acceptable grain yield.
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21
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Maurya J, Bandyopadhyay T, Prasad M. Transcriptional regulators of nitrate metabolism: Key players in improving nitrogen use in crops. J Biotechnol 2020; 324:121-133. [PMID: 33031844 DOI: 10.1016/j.jbiotec.2020.10.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 08/19/2020] [Accepted: 10/03/2020] [Indexed: 11/30/2022]
Abstract
Green revolution has boosted crop yields by the development of varieties which rely on high fertilizer application. Since then, higher productivity has largely witnessed excessive nitrogen (N) fertilizer application resulting in many environmentally and agronomically unsustainable consequences. One possible solution to this problem is to develop varieties with efficient N use endowed with genetically superior N metabolizing machinery, thereby significantly reducing N loss in soil and facilitating gainful yield performance at lower N conditions. Nitrate (NO3-) is the major form of N acquired by plants in aerobic soils. Hence, its efficient acquisition, transport, assimilation into complex organic compounds, and overall homeostasis is crucial to ensure productivity under optimal and suboptimal N conditions. Transcription factors are prime regulators of these processes, and insights into their mechanism of action and the resultant effect on N metabolism are crucial to generating crops with efficient and durable nitrogen use efficiency. The present review, therefore, presents a comprehensive updated account of major N responsive transcription factor families, their cross-talk with other growth factors, and explores existing and potential areas of their biotechnological application to maximize crop yields.
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Affiliation(s)
- Jyoti Maurya
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | | | - Manoj Prasad
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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Plett DC, Ranathunge K, Melino VJ, Kuya N, Uga Y, Kronzucker HJ. The intersection of nitrogen nutrition and water use in plants: new paths toward improved crop productivity. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:4452-4468. [PMID: 32026944 PMCID: PMC7382376 DOI: 10.1093/jxb/eraa049] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 02/05/2020] [Indexed: 05/19/2023]
Abstract
Water and nitrogen availability limit crop productivity globally more than most other environmental factors. Plant availability of macronutrients such as nitrate is, to a large extent, regulated by the amount of water available in the soil, and, during drought episodes, crops can become simultaneously water and nitrogen limited. In this review, we explore the intricate relationship between water and nitrogen transport in plants, from transpiration-driven mass flow in the soil to uptake by roots via membrane transporters and channels and transport to aerial organs. We discuss the roles of root architecture and of suberized hydrophobic root barriers governing apoplastic water and nitrogen movement into the vascular system. We also highlight the need to identify the signalling cascades regulating water and nitrogen transport, as well as the need for targeted physiological analyses of plant traits influencing water and nitrogen uptake. We further advocate for incorporation of new phenotyping technologies, breeding strategies, and agronomic practices to improve crop yield in water- and nitrogen-limited production systems.
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Affiliation(s)
- Darren C Plett
- School of Agriculture and Food, The University of Melbourne, Melbourne, VIC, Australia
| | - Kosala Ranathunge
- School of Biological Sciences, University of Western Australia, Crawley, Perth, Australia
| | - Vanessa J Melino
- School of Agriculture and Food, The University of Melbourne, Melbourne, VIC, Australia
| | - Noriyuki Kuya
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
| | - Yusaku Uga
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
| | - Herbert J Kronzucker
- School of Agriculture and Food, The University of Melbourne, Melbourne, VIC, Australia
- Faculty of Land and Food Systems, University of British Columbia, Vancouver, British Columbia, Canada
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23
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Srivastava AK, Shankar A, Nalini Chandran AK, Sharma M, Jung KH, Suprasanna P, Pandey GK. Emerging concepts of potassium homeostasis in plants. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:608-619. [PMID: 31624829 DOI: 10.1093/jxb/erz458] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Accepted: 10/03/2019] [Indexed: 06/10/2023]
Abstract
Potassium (K+) is an essential cation in all organisms that influences crop production and ecosystem stability. Although most soils are rich in K minerals, relatively little K+ is present in forms that are available to plants. Moreover, leaching and run-off from the upper soil layers contribute to K+ deficiencies in agricultural soils. Hence, the demand for K fertilizer is increasing worldwide. K+ regulates multiple processes in cells and organs, with K+ deficiency resulting in decreased plant growth and productivity. Here, we discuss the complexity of the reactive oxygen species-calcium-hormone signalling network that is responsible for the sensing of K+ deficiency in plants, together with genetic approaches using K+ transporters that have been used to increase K+ use efficiency (KUE) in plants, particularly under environmental stress conditions such as salinity and heavy metal contamination. Publicly available rice transcriptome data are used to demonstrate the two-way relationship between K+ and nitrogen nutrition, highlighting how each nutrient can regulate the uptake and root to shoot translocation of the other. Future research directions are discussed in terms of this relationship, as well as prospects for molecular approaches for the generation of improved varieties and the implementation of new agronomic practices. An increased knowledge of the systems that sense and take up K+, and their regulation, will not only improve current understanding of plant K+ homeostasis but also facilitate new research and the implementation of measures to improve plant KUE for sustainable food production.
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Affiliation(s)
- Ashish Kumar Srivastava
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Alka Shankar
- Department of Plant Molecular Biology, University of Delhi South Campus, Dhaula Kuan, New Delhi, India
| | - Anil Kumar Nalini Chandran
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, Republic of Korea
| | - Manisha Sharma
- Department of Plant Molecular Biology, University of Delhi South Campus, Dhaula Kuan, New Delhi, India
| | - Ki-Hong Jung
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, Republic of Korea
| | - Penna Suprasanna
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Girdhar K Pandey
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, India
- Department of Plant Molecular Biology, University of Delhi South Campus, Dhaula Kuan, New Delhi, India
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Zuluaga DL, Sonnante G. The Use of Nitrogen and Its Regulation in Cereals: Structural Genes, Transcription Factors, and the Role of miRNAs. PLANTS 2019; 8:plants8080294. [PMID: 31434274 PMCID: PMC6724420 DOI: 10.3390/plants8080294] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 08/15/2019] [Accepted: 08/16/2019] [Indexed: 01/31/2023]
Abstract
Cereals and, especially, rice, maize, and wheat, are essential commodities, on which human nutrition is based. Expanding population and food demand have required higher production which has been achieved by increasing fertilization, and especially nitrogen supply to cereal crops. In fact, nitrogen is a crucial nutrient for the plant, but excessive use poses serious environmental and health issues. Therefore, increasing nitrogen use efficiency in cereals is of pivotal importance for sustainable agriculture. The main steps in the use of nitrogen are uptake and transport, reduction and assimilation, and translocation and remobilization. Many studies have been carried out on the genes involved in these phases, and on transcription factors regulating these genes. Lately, increasing attention has been paid to miRNAs responding to abiotic stress, including nutrient deficiency. Many miRNAs have been found to regulate transcription factors acting on the expression of specific genes for nitrogen uptake or remobilization. Recent studies on gene regulatory networks have also demonstrated that miRNAs can interact with several nodes in the network, functioning as key regulators in nitrogen metabolism.
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Affiliation(s)
- Diana L Zuluaga
- Institute of Biosciences and Bioresources, National Research Council, Via Amendola 165/A, 70126 Bari, Italy.
| | - Gabriella Sonnante
- Institute of Biosciences and Bioresources, National Research Council, Via Amendola 165/A, 70126 Bari, Italy.
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25
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Wang P, Wang Z, Pan Q, Sun X, Chen H, Chen F, Yuan L, Mi G. Increased biomass accumulation in maize grown in mixed nitrogen supply is mediated by auxin synthesis. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:1859-1873. [PMID: 30759246 PMCID: PMC6436159 DOI: 10.1093/jxb/erz047] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Accepted: 01/23/2019] [Indexed: 05/16/2023]
Abstract
The use of mixed nitrate and ammonium as a nitrogen source can improve plant growth. Here, we used metabolomics and transcriptomics to study the underlying mechanisms. Maize plants were grown hydroponically in the presence of three forms of nitrogen (nitrate alone, 75%/25% nitrate/ammonium, and ammonium alone). Plants grown with mixed nitrogen had a higher photosynthetic rate than those supplied only with nitrate, and had the highest leaf area and shoot and root biomass among the three nitrogen treatments. In shoot and root, the concentration of nitrogenous compounds (ammonium, glutamine, and asparagine) and carbohydrates (sucrose, glucose, and fructose) in plants with a mixed nitrogen supply was higher than that with nitrate supply, but lower than that with ammonium supply. The activity of the related enzymes (glutamate synthase, asparagine synthase, phosphoenolpyruvate carboxylase, invertase, and ADP-glucose pyrophosphorylase) changed accordingly. Specifically, the mixed nitrogen source enhanced auxin synthesis via the shikimic acid pathway, as indicated by the higher levels of phosphoenolpyruvate and tryptophan compared with the other two treatments. The expression of corresponding genes involving auxin synthesis and response was up-regulated. Supply of only ammonium resulted in high levels of glutamine and asparagine, starch, and trehalose hexaphosphate. We conclude that, in addition to increased photosynthesis, mixed nitrogen supply enhances leaf growth via increasing auxin synthesis to build a large sink for carbon and nitrogen utilization, which, in turn, facilitates further carbon assimilation and nitrogen uptake.
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Affiliation(s)
- Peng Wang
- Department of Plant Nutrition, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Zhangkui Wang
- Department of Plant Nutrition, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Qingchun Pan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Xichao Sun
- Department of Plant Nutrition, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Huan Chen
- Department of Plant Nutrition, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Fanjun Chen
- Department of Plant Nutrition, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Lixing Yuan
- Department of Plant Nutrition, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Guohua Mi
- Department of Plant Nutrition, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
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26
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Nawaz MA, Chen C, Shireen F, Zheng Z, Sohail H, Afzal M, Ali MA, Bie Z, Huang Y. Genome-wide expression profiling of leaves and roots of watermelon in response to low nitrogen. BMC Genomics 2018; 19:456. [PMID: 29898660 PMCID: PMC6001020 DOI: 10.1186/s12864-018-4856-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 06/06/2018] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Nitrogen (N) is a key macronutrient required for plant growth and development. In this study, watermelon plants were grown under hydroponic conditions at 0.2 mM N, 4.5 mM N, and 9 mM N for 14 days. RESULTS Dry weight and photosynthetic assimilation at low N (0.2 mM) was reduced by 29 and 74% compared with high N (9 mM). The photochemical activity (Fv/Fm) was also reduced from 0.78 at high N to 0.71 at low N. The N concentration in the leaf, stem, and root of watermelon under low N conditions was reduced by 68, 104, and 108%, respectively compared with 9 mM N treatment after 14 days of N treatment. In the leaf tissues of watermelon grown under low N conditions, 9598 genes were differentially expressed, out of which 4533 genes (47.22%) were up-regulated whereas, 5065 genes (52.78%) were down-regulated compared with high N. Similarly in the root tissues, 3956 genes were differentially expressed, out of which 1605 genes were up-regulated (40.57%) and 2351 genes were down-regulated (59.43%), compared with high N. Our results suggest that leaf tissues are more sensitive to N deficiency compared with root tissues. The gene ontology (GO) analysis showed that the availability of N significantly affected 19 biological processes, 8 cell component metabolic pathways, and 3 molecular functions in the leaves; and 13 biological processes, 12 molecular functions, and 5 cell component metabolic pathways in the roots of watermelon. The low affinity nitrate transporters, high affinity nitrate transporters, ammonium transporters, genes related with nitrogen assimilation, and chlorophyll and photosynthesis were expressed differentially in response to low N. Three nitrate transporters (Cla010066, Cla009721, Cla012765) substantially responded to low nitrate supply in the root and leaf tissues. Additionally, a large number of transcription factors (1365) were involved in adaptation to low N availability. The major transcription factor families identified in this study includes MYB, AP2-EREBP, bHLH, C2H2 and NAC. CONCLUSION Candidate genes identified in this study for nitrate uptake and transport can be targeted and utilized for further studies in watermelon breeding and improvement programs to improve N uptake and utilization efficiency.
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Affiliation(s)
- Muhammad Azher Nawaz
- Key Laboratory of Horticultural Plant Biology, Ministry of Education/College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
- University College of Agriculture, University of Sargodha, Sargodha, Pakistan
| | - Chen Chen
- Key Laboratory of Horticultural Plant Biology, Ministry of Education/College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Fareeha Shireen
- Key Laboratory of Horticultural Plant Biology, Ministry of Education/College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Zhuhua Zheng
- Key Laboratory of Horticultural Plant Biology, Ministry of Education/College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Hamza Sohail
- Key Laboratory of Horticultural Plant Biology, Ministry of Education/College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Muhammad Afzal
- University College of Agriculture, University of Sargodha, Sargodha, Pakistan
| | - Muhammad Amjad Ali
- Department of Plant Pathology, and Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan
| | - Zhilong Bie
- Key Laboratory of Horticultural Plant Biology, Ministry of Education/College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Yuan Huang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education/College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
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