1
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Xu Q, Wang Y, Sun W, Li Y, Xu Y, Cheng B, Li X. Genome-wide identification of nitrate transporter 1/peptide transporter family ( NPF) induced by arbuscular mycorrhiza in the maize genome. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2024; 30:757-774. [PMID: 38846454 PMCID: PMC11150374 DOI: 10.1007/s12298-024-01464-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 04/27/2024] [Accepted: 05/15/2024] [Indexed: 06/09/2024]
Abstract
The Transporter 1/Peptide Transporter Family (NPF) is essential for the uptake and transport of nitrate nitrogen. Significant increases in nitrogen have been increasingly reported for many mycorrhizal plants, but there are few reports on maize. Here, we have identified the maize NPF family and screened for arbuscular mycorrhiza fungi (AMF) induced NPFs. In this study, a systematic analysis of the maize NPF gene family was performed. A total of 82 NPF genes were identified in maize. ZmNPF4.5 was strongly induced by AMF in both low and high nitrogen. Lotus japonicus hairy root-induced transformation experiments showed that ZmNPF4.5 promoter-driven GUS activity was restricted to cells containing tufts. Yeast backfill experiments indicate that ZmNPF4.5 functions in nitrate uptake. Therefore, we speculate that ZmNPF4.5 is a key gene for nitrate-nitrogen uptake in maize through the mycorrhizal pathway. This is a reference value for further exploring the acquisition of nitrate-nitrogen by maize through AMF pathway. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-024-01464-3.
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Affiliation(s)
- Qiang Xu
- Key Laboratory of Crop Stress Resistance and High Quality Biology of Anhui Province, Anhui Agricultural University, Hefei, China
| | - Yanping Wang
- Key Laboratory of Crop Stress Resistance and High Quality Biology of Anhui Province, Anhui Agricultural University, Hefei, China
| | - Wen Sun
- Key Laboratory of Crop Stress Resistance and High Quality Biology of Anhui Province, Anhui Agricultural University, Hefei, China
| | - Yuanhao Li
- Key Laboratory of Crop Stress Resistance and High Quality Biology of Anhui Province, Anhui Agricultural University, Hefei, China
| | - Yunjian Xu
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, China
| | - Beijiu Cheng
- Key Laboratory of Crop Stress Resistance and High Quality Biology of Anhui Province, Anhui Agricultural University, Hefei, China
| | - Xiaoyu Li
- Key Laboratory of Crop Stress Resistance and High Quality Biology of Anhui Province, Anhui Agricultural University, Hefei, China
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2
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Li Q, Song HL, Zhou T, Pei MN, Wang B, Yan SX, Liu YQ, Wu PJ, Hua YP. Differential Morpho-Physiological, Ionomic, and Phytohormone Profiles, and Genome-Wide Expression Profiling Involving the Tolerance of Allohexaploid Wheat ( Triticum aestivum L.) to Nitrogen Limitation. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:3814-3831. [PMID: 38329036 DOI: 10.1021/acs.jafc.3c08626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Common wheat (Triticum aestivum L.) is a global staple food, while nitrogen (N) limitation severely hinders plant growth, seed yield, and grain quality of wheat. Genetic variations in the responses to low N stresses among allohexaploid wheat (AABBDD, 2n = 6x = 42) genotypes emphasize the complicated regulatory mechanisms underlying low N tolerance and N use efficiency (NUE). In this study, hydroponic culture, inductively coupled plasma mass spectrometry, noninvasive microtest, high-performance liquid chromatography, RNA-seq, and bioinformatics were used to determine the differential growth performance, ionome and phytohormone profiles, and genome-wide expression profiling of wheat plants grown under high N and low N conditions. Transcriptional profiling of NPFs, NRT2s, CLCs, SLACs/SLAHs, AAPs, UPSs, NIAs, and GSs characterized the core members, such as TaNPF6.3-6D, TaNRT2.3-3D, TaNIA1-6B, TaGLN1;2-4B, TaAAP14-5A/5D, and TaUPS2-5A, involved in the efficient transport and assimilation of nitrate and organic N nutrients. The low-N-sensitivity wheat cultivar XM26 showed obvious leaf chlorosis and accumulated higher levels of ABA, JA, and SA than the low-N-tolerant ZM578 under N limitation. The TaMYB59-3D-TaNPF7.3/NRT1.5-6D module-mediated shoot-to-root translocation and leaf remobilization of nitrate was proposed as an important pathway regulating the differential responses between ZM578 and XM26 to low N. This study provides some elite candidate genes for the selection and breeding of wheat germplasms with low N tolerance and high NUE.
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Affiliation(s)
- Qiong Li
- Department of Brewing Engineering, Moutai Institute, Renhuai 564507, Guizhou, China
| | - Hai-Li Song
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Ting Zhou
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Min-Nan Pei
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Bing Wang
- Department of Brewing Engineering, Moutai Institute, Renhuai 564507, Guizhou, China
| | - Song-Xian Yan
- Department of Resources and Environment, Moutai Institute, Renhuai 564507, Guizhou, China
| | - Yun-Qi Liu
- Zhongguancun Xuyue Non-invasive Micro-test Technology Industrial Alliance, Beijing 10080, China
| | - Peng-Jia Wu
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Ying-Peng Hua
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
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Feng Y, Ma X, Yang Y, Tao S, Ahmed A, Gong Z, Cheng X, Zhang W. The roles of DNA methylation on pH dependent i-motif (iM) formation in rice. Nucleic Acids Res 2024; 52:1243-1257. [PMID: 38180820 PMCID: PMC10853798 DOI: 10.1093/nar/gkad1245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 12/14/2023] [Accepted: 12/19/2023] [Indexed: 01/07/2024] Open
Abstract
I-motifs (iMs) are four-stranded non-B DNA structures containing C-rich DNA sequences. The formation of iMs is sensitive to pH conditions and DNA methylation, although the extent of which is still unknown in both humans and plants. To investigate this, we here conducted iMab antibody-based immunoprecipitation and sequencing (iM-IP-seq) along with bisulfite sequencing using CK (original genomic DNA without methylation-related treatments) and hypermethylated or demethylated DNA at both pH 5.5 and 7.0 in rice, establishing a link between pH, DNA methylation and iM formation on a genome-wide scale. We found that iMs folded at pH 7.0 displayed higher methylation levels than those formed at pH 5.5. DNA demethylation and hypermethylation differently influenced iM formation at pH 7.0 and 5.5. Importantly, CG hypo-DMRs (differentially methylated regions) and CHH (H = A, C and T) hyper-DMRs alone or coordinated with CG/CHG hyper-DMRs may play determinant roles in the regulation of pH dependent iM formation. Thus, our study shows that the nature of DNA sequences alone or combined with their methylation status plays critical roles in determining pH-dependent formation of iMs. It therefore deepens the understanding of the pH and methylation dependent modulation of iM formation, which has important biological implications and practical applications.
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Affiliation(s)
- Yilong Feng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, CIC-MCP, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, China
| | - Xing Ma
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, CIC-MCP, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, China
| | - Ying Yang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, CIC-MCP, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, China
| | - Shentong Tao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, CIC-MCP, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, China
| | - Asgar Ahmed
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, CIC-MCP, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, China
- Bangladesh Wheat and Maize Research Institute (BWMRI), Nashipur, Dinajpur 5200, Bangladesh
| | - Zhiyun Gong
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou 225009, China
| | - Xuejiao Cheng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, CIC-MCP, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, China
| | - Wenli Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, CIC-MCP, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, China
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Chen B, Shi Y, Lu L, Wang L, Sun Y, Ning W, Liu Z, Cheng S. PsNRT2.3 interacts with PsNAR to promote high-affinity nitrate uptake in pea (Pisum sativum L.). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 206:108191. [PMID: 38016367 DOI: 10.1016/j.plaphy.2023.108191] [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: 07/25/2023] [Revised: 11/06/2023] [Accepted: 11/10/2023] [Indexed: 11/30/2023]
Abstract
Nitrate, the primary form of nitrogen absorbed by plants, supplies essential compounds for plant growth and development. Peas are frequently used as rotation crops to improve and stabilize soil fertility. However, the determinants of nitrate uptake and transport in peas remain largely unclear, primarily due to the pea genome's complexity and size. In this study, we utilized the complete genomic information of peas to identify three PsNRT2 family genes within the pea genome. We conducted a comprehensive examination of their protein conserved domains, physicochemical properties, gene structure, and phylogenetic evolution, revealing PsNRT2.3 as the potential key gene for high-affinity nitrate transport in peas. Subcellular localization studies indicated that PsNRT2.3 resides on the plasma membrane. Using hairy root transformation, we noted the predominant expression of PsNRT2.3 in the root stele, which is inducible by nitrate. Our experiments involving overexpression and silencing methods further confirmed that PsNRT2.3 plays a key role in enhancing nitrate uptake in peas. Additionally, our work showed that PsNAR could interact with PsNRT2.3, modulating pea nitrate uptake. After silencing PsNAR, even with the normal expression of PsNRT2.3, the ability of peas to absorb nitrate was significantly reduced. In conclusion, this study identifies the high-affinity nitrate transport gene PsNRT2.3 in peas and clarifies its critical role and regulatory network in nitrate transport, contributing to a new understanding of nitrate utilization in peas.
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Affiliation(s)
- Baizhi Chen
- Agricultural Genomics Institute at Shenzhen (AGIS), Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, China
| | - Yan Shi
- Agricultural Genomics Institute at Shenzhen (AGIS), Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, China
| | - Lu Lu
- Agricultural Genomics Institute at Shenzhen (AGIS), Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, China; State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China; Shenzhen Research Institute of Henan University, Shenzhen, 518000, China
| | - Luyao Wang
- Agricultural Genomics Institute at Shenzhen (AGIS), Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, China; College of Agronomy, Shanxi Agricultural University, Taigu, China
| | - Yuchen Sun
- Agricultural Genomics Institute at Shenzhen (AGIS), Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, China
| | - Weidong Ning
- Agricultural Genomics Institute at Shenzhen (AGIS), Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, China
| | - Zijian Liu
- Agricultural Genomics Institute at Shenzhen (AGIS), Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, China
| | - Shifeng Cheng
- Agricultural Genomics Institute at Shenzhen (AGIS), Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, China.
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5
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Sigalas PP, Buchner P, Kröper A, Hawkesford MJ. The Functional Diversity of the High-Affinity Nitrate Transporter Gene Family in Hexaploid Wheat: Insights from Distinct Expression Profiles. Int J Mol Sci 2023; 25:509. [PMID: 38203680 PMCID: PMC10779101 DOI: 10.3390/ijms25010509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 12/22/2023] [Accepted: 12/23/2023] [Indexed: 01/12/2024] Open
Abstract
High-affinity nitrate transporters (NRT) are key components for nitrogen (N) acquisition and distribution within plants. However, insights on these transporters in wheat are scarce. This study presents a comprehensive analysis of the NRT2 and NRT3 gene families, where the aim is to shed light on their functionality and to evaluate their responses to N availability. A total of 53 NRT2s and 11 NRT3s were identified in the bread wheat genome, and these were grouped into different clades and homoeologous subgroups. The transcriptional dynamics of the identified NRT2 and NRT3 genes, in response to N starvation and nitrate resupply, were examined by RT-qPCR in the roots and shoots of hydroponically grown wheat plants through a time course experiment. Additionally, the spatial expression patterns of these genes were explored within the plant. The NRT2s of clade 1, TaNRT2.1-2.6, showed a root-specific expression and significant upregulation in response to N starvation, thus emphasizing a role in N acquisition. However, most of the clade 2 NRT2s displayed reduced expression under N-starved conditions. Nitrate resupply after N starvation revealed rapid responsiveness in TaNRT2.1-2.6, while clade 2 genes exhibited gradual induction, primarily in the roots. TaNRT2.18 was highly expressed in above-ground tissues and exhibited distinct nitrate-related response patterns for roots and shoots. The TaNRT3 gene expression closely paralleled the profiles of TaNRT2.1-2.6 in response to nitrate induction. These findings enhance the understanding of NRT2 and NRT3 involvement in nitrogen uptake and utilization, and they could have practical implications for improving nitrogen use efficiency. The study also recommends a standardized nomenclature for wheat NRT2 genes, thereby addressing prior naming inconsistencies.
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Affiliation(s)
- Petros P. Sigalas
- Rothamsted Research, West Common, Harpenden AL5 2JQ, UK; (P.B.); (M.J.H.)
| | - Peter Buchner
- Rothamsted Research, West Common, Harpenden AL5 2JQ, UK; (P.B.); (M.J.H.)
| | - Alex Kröper
- Faculty of Agronomy, University of Hohenheim, 70599 Stuttgart, Germany;
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Li D, Wu X, Huang C, Lin Q, Wang Y, Yang X, Wang C, Xuan Y, Wei S, Mei Q. Enhanced Rice Resistance to Sheath Blight through Nitrate Transporter 1.1B Mutation without Yield Loss under NH 4+ Fertilization. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:19958-19969. [PMID: 38085756 DOI: 10.1021/acs.jafc.3c05350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Nitrogen fertilization can promote rice yield but decrease resistance to sheath blight (ShB). In this study, the nitrate transporter 1.1b (nrt1.1b) mutant that exhibited less susceptibility to ShB but without compromising yield under NH4+ fertilization was screened. NRT1.1B's regulation of ShB resistance was independent of the total nitrogen concentration in rice under NH4+ conditions. In nrt1.1b mutant plants, the NH4+ application modulated auxin signaling, chlorophyll content, and phosphate signaling to promote ShB resistance. Furthermore, the findings indicated that NRT1.1B negatively regulated ShB resistance by positively modulating the expression of H+-ATPase gene OSA3 and phosphate transport gene PT8. The mutation of OSA3 and PT8 promoted ShB resistance by increasing the apoplastic pH in rice. Our study identified the ShB resistance mutant nrt1.1b, which maintained normal nitrogen use efficiency without compromising yield.
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Affiliation(s)
- Dandan Li
- College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning 110866, People's Republic of China
| | - Xianxin Wu
- Institute of Agricultural Quality Standards and Testing Technology, Liaoning Academy of Agricultural Sciences, Shenyang, Liaoning 110161, People's Republic of China
| | - Chunyan Huang
- College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning 110866, People's Republic of China
| | - Qiujun Lin
- Institute of Agricultural Quality Standards and Testing Technology, Liaoning Academy of Agricultural Sciences, Shenyang, Liaoning 110161, People's Republic of China
| | - Yan Wang
- College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning 110866, People's Republic of China
| | - Xu Yang
- Microelement Research Center, College of Resources & Environment, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Chuang Wang
- Microelement Research Center, College of Resources & Environment, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Yuanhu Xuan
- College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning 110866, People's Republic of China
| | - Songhong Wei
- College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning 110866, People's Republic of China
| | - Qiong Mei
- College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning 110866, People's Republic of China
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Deng QY, Luo JT, Zheng JM, Tan WF, Pu ZJ, Wang F. Genome-wide systematic characterization of the NRT2 gene family and its expression profile in wheat (Triticum aestivum L.) during plant growth and in response to nitrate deficiency. BMC PLANT BIOLOGY 2023; 23:353. [PMID: 37420192 DOI: 10.1186/s12870-023-04333-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 06/06/2023] [Indexed: 07/09/2023]
Abstract
BACKGROUND Wheat (Triticum aestivum L.) is a major cereal crop that is grown worldwide, and it is highly dependent on sufficient N supply. The molecular mechanisms associated with nitrate uptake and assimilation are still poorly understood in wheat. In plants, NRT2 family proteins play a crucial role in NO3- acquisition and translocation under nitrate limited conditions. However, the biological functions of these genes in wheat are still unclear, especially their roles in NO3- uptake and assimilation. RESULTS In this study, a comprehensive analysis of wheat TaNRT2 genes was conducted using bioinformatics and molecular biology methods, and 49 TaNRT2 genes were identified. A phylogenetic analysis clustered the TaNRT2 genes into three clades. The genes that clustered on the same phylogenetic branch had similar gene structures and nitrate assimilation functions. The identified genes were further mapped onto the 13 wheat chromosomes, and the results showed that a large duplication event had occurred on chromosome 6. To explore the TaNRT2 gene expression profiles in wheat, we performed transcriptome sequencing after low nitrate treatment for three days. Transcriptome analysis revealed the expression levels of all TaNRT2 genes in shoots and roots, and based on the expression profiles, three highly expressed genes (TaNRT2-6A.2, TaNRT2-6A.6, and TaNRT2-6B.4) were selected for qPCR analysis in two different wheat cultivars ('Mianmai367' and 'Nanmai660') under nitrate-limited and normal conditions. All three genes were upregulated under nitrate-limited conditions and highly expressed in the high nitrogen use efficiency (NUE) wheat 'Mianmai367' under low nitrate conditions. CONCLUSION We systematically identified 49 NRT2 genes in wheat and analysed the transcript levels of all TaNRT2s under nitrate deficient conditions and over the whole growth period. The results suggest that these genes play important roles in nitrate absorption, distribution, and accumulation. This study provides valuable information and key candidate genes for further studies on the function of TaNRT2s in wheat.
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Affiliation(s)
- Qing-Yan Deng
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, China
- Environment-Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu, 610066, Sichuan, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China (Ministry of Agriculture and Rural Affairs of P.R.C.), Chengdu, Sichuan, 610066, China
| | - Jiang-Tao Luo
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, China
- Environment-Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu, 610066, Sichuan, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China (Ministry of Agriculture and Rural Affairs of P.R.C.), Chengdu, Sichuan, 610066, China
| | - Jian-Min Zheng
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, China
- Environment-Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu, 610066, Sichuan, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China (Ministry of Agriculture and Rural Affairs of P.R.C.), Chengdu, Sichuan, 610066, China
| | - Wen-Fang Tan
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, China.
- Environment-Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu, 610066, Sichuan, China.
| | - Zong-Jun Pu
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, China.
- Environment-Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu, 610066, Sichuan, China.
- Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China (Ministry of Agriculture and Rural Affairs of P.R.C.), Chengdu, Sichuan, 610066, China.
| | - Fang Wang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, China.
- Environment-Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu, 610066, Sichuan, China.
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8
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Schmidt L, Jacobs J, Schmutzer T, Alqudah AM, Sannemann W, Pillen K, Maurer A. Identifying genomic regions determining shoot and root traits related to nitrogen uptake efficiency in a multiparent advanced generation intercross (MAGIC) winter wheat population in a high-throughput phenotyping facility. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 330:111656. [PMID: 36841338 DOI: 10.1016/j.plantsci.2023.111656] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 01/17/2023] [Accepted: 02/18/2023] [Indexed: 06/18/2023]
Abstract
In the context of a continuously increasing human population that needs to be fed, with environmental protection in mind, nitrogen use efficiency (NUE) improvement is becoming very important. To understand the natural variation of traits linked to nitrogen uptake efficiency (UPE), one component of NUE, the multiparent advanced generation intercross (MAGIC) winter wheat population WM-800 was phenotyped under two contrasting nitrogen (N) levels in a high-throughput phenotyping facility for six weeks. Three biomass-related, three root-related, and two reflectance-related traits were measured weekly under each treatment. Subsequently, the population was genetically analysed using a total of 13,060 polymorphic haplotypes and singular SNPs for a genome-wide association study (GWAS). In total, we detected 543 quantitative trait loci (QTL) across all time points and traits, which were pooled into 42 stable QTL (sQTL; present in at least three of the six weeks). Besides Rht-B1 and Rht-D1, candidate genes playing a role in gibberellic acid-regulated growth and nitrate transporter genes from the NPF gene family, like NRT 1.1, were linked to sQTL. Two novel sQTL on chromosomes 5 A and 6D showed pleiotropic effects on several traits. The high number of N-specific sQTL indicates that selection for UPE is useful specifically under N-limited conditions.
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Affiliation(s)
- Laura Schmidt
- Martin Luther University Halle-Wittenberg, Chair of Plant Breeding, Betty-Heimann-Str. 3, 06120 Halle, Germany
| | - John Jacobs
- BASF BBCC Innovation Center Gent, 9052 Gent, Belgium
| | - Thomas Schmutzer
- Martin Luther University Halle-Wittenberg, Chair of Plant Breeding, Betty-Heimann-Str. 3, 06120 Halle, Germany
| | - Ahmad M Alqudah
- Martin Luther University Halle-Wittenberg, Chair of Plant Breeding, Betty-Heimann-Str. 3, 06120 Halle, Germany; Biological Science Program, Department of Biological and Environmental Sciences, College of Art and Science, Qatar University, P.O. Box 2713, Doha, Qatar
| | - Wiebke Sannemann
- Martin Luther University Halle-Wittenberg, Chair of Plant Breeding, Betty-Heimann-Str. 3, 06120 Halle, Germany
| | - Klaus Pillen
- Martin Luther University Halle-Wittenberg, Chair of Plant Breeding, Betty-Heimann-Str. 3, 06120 Halle, Germany
| | - Andreas Maurer
- Martin Luther University Halle-Wittenberg, Chair of Plant Breeding, Betty-Heimann-Str. 3, 06120 Halle, Germany.
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9
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Zhang X, Feng J, Zhao R, Cheng H, Ashraf J, Wang Q, Lv L, Zhang Y, Song G, Zuo D. Functional characterization of the GhNRT2.1e gene reveals its significant role in improving nitrogen use efficiency in Gossypium hirsutum. PeerJ 2023; 11:e15152. [PMID: 37009157 PMCID: PMC10064996 DOI: 10.7717/peerj.15152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 03/10/2023] [Indexed: 03/30/2023] Open
Abstract
Background
Nitrate is the primary type of nitrogen available to plants, which is absorbed and transported by nitrate transporter 2 (NRT2) at low nitrate conditions.
Methods
Genome-wide identification of NRT2 genes in G. hirsutum was performed. Gene expression patterns were revealed using RNA-seq and qRT-PCR. Gene functions were characterized using overexpression in A. thaliana and silencing in G. hirsutum. Protein interactions were verified by yeast two-hybrid and luciferase complementation imaging (LCI) assays.
Results
We identified 14, 14, seven, and seven NRT2 proteins in G. hirsutum, G. barbadense, G. raimondii, and G. arboreum. Most NRT2 proteins were predicted in the plasma membrane. The NRT2 genes were classified into four distinct groups through evolutionary relationships, with members of the same group similar in conserved motifs and gene structure. The promoter regions of NRT2 genes included many elements related to growth regulation, phytohormones, and abiotic stresses. Tissue expression pattern results revealed that most GhNRT2 genes were specifically expressed in roots. Under low nitrate conditions, GhNRT2 genes exhibited different expression levels, with GhNRT2.1e being the most up-regulated. Arabidopsis plants overexpressing GhNRT2.1e exhibited increased biomass, nitrogen and nitrate accumulation, nitrogen uptake and utilization efficiency, nitrogen-metabolizing enzyme activity, and amino acid content under low nitrate conditions. In addition, GhNRT2.1e-silenced plants exhibited suppressed nitrate uptake and accumulation, hampered plant growth, affected nitrogen metabolism processes, and reduced tolerance to low nitrate. The results showed that GhNRT2.1e could promote nitrate uptake and transport under low nitrate conditions, thus effectively increasing nitrogen use efficiency (NUE). We found that GhNRT2.1e interacts with GhNAR2.1 by yeast two-hybrid and LCI assays.
Discussion
Our research lays the foundation to increase NUE and cultivate new cotton varieties with efficient nitrogen use.
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Affiliation(s)
- Xinmiao Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Jiajia Feng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Ruolin Zhao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Hailiang Cheng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Javaria Ashraf
- Department of Plant Breeding and Genetics, Faculty of Agriculture and Environment, The Islamia University of Bahawalpur, Bahawalpur, Punjab, Pakistan
| | - Qiaolian Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Limin Lv
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Youping Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Guoli Song
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Dongyun Zuo
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
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Pu Y, Wang P, Abbas M, Khan MA, Xu J, Yang Y, Zhou T, Zheng K, Chen Q, Sun G. Genome-wide identification and analyses of cotton high-affinity nitrate transporter 2 family genes and their responses to stress. FRONTIERS IN PLANT SCIENCE 2023; 14:1170048. [PMID: 37089653 PMCID: PMC10113457 DOI: 10.3389/fpls.2023.1170048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 03/22/2023] [Indexed: 05/03/2023]
Abstract
Nitrate transporters (NRTs) are crucial for the uptake, use, and storage of nitrogen by plants. In this study, 42 members of the GhNRT2 (Nitrate Transporter 2 family) were found in the four different cotton species. The conserved domains, phylogenetic relationships, physicochemical properties, subcellular localization, conserved motifs, gene structure, cis-acting elements, and promoter region expression patterns of these 42 members were analyzed. The findings confirmed that members of the NRT2 family behaved typically, and subcellular localization tests confirmed that they were hydrophobic proteins that were mostly located on the cytoplasmic membrane. The NRT2 family of genes with A.thaliana and rice underwent phylogenetic analysis, and the results revealed that GhNRT2 could be divided into three groups. The same taxa also shared similar gene structure and motif distribution. The composition of cis-acting elements suggests that most of the expression of GhNRT2 may be related to plant hormones, abiotic stress, and photoreactions. The GhNRT2 gene was highly expressed, mainly in roots. Drought, salt, and extreme temperature stress showed that GhNRT2 gene expression was significantly up-regulated or down-regulated, indicating that it may be involved in the stress response of cotton. In general, the genes of the NRT2 family of cotton were comprehensively analyzed, and their potential nitrogen uptake and utilization functions in cotton were preliminarily predicted. Additionally, we provide an experimental basis for the adverse stress conditions in which they may function.
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Affiliation(s)
- Yuanchun Pu
- College of Agronomy, Xinjiang Agricultural University, Urumqi, China
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Peilin Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mubashir Abbas
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Muhammad Aamir Khan
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jiangling Xu
- College of Agronomy, Xinjiang Agricultural University, Urumqi, China
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yejun Yang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Agronomy, Shanxi Agricultural University, Jinzhong, China
| | - Ting Zhou
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Agronomy, Shanxi Agricultural University, Jinzhong, China
| | - Kai Zheng
- College of Agronomy, Xinjiang Agricultural University, Urumqi, China
| | - Quanjia Chen
- College of Agronomy, Xinjiang Agricultural University, Urumqi, China
- *Correspondence: Quanjia Chen, ; Guoqing Sun,
| | - Guoqing Sun
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Quanjia Chen, ; Guoqing Sun,
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11
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Rogato A, Valkov VT, Chiurazzi M. LjNRT2.3 plays a hierarchical role in the control of high affinity transport system for root nitrate acquisition in Lotus japonicus. FRONTIERS IN PLANT SCIENCE 2022; 13:1042513. [PMID: 36438153 PMCID: PMC9687105 DOI: 10.3389/fpls.2022.1042513] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 10/25/2022] [Indexed: 06/16/2023]
Abstract
Nitrate is a key mineral nutrient required for plant growth and development. Plants have evolved sophisticated mechanisms to respond to changes of nutritional availability in the surrounding environment and the optimization of root nitrate acquisition under nitrogen starvation is crucial to cope with unfavoured condition of growth. In this study we present a general description of the regulatory transcriptional and spatial profile of expression of the Lotus japonicus nitrate transporter NRT2 family. Furthermore, we report a phenotypic characterization of two independent Ljnrt2.3 knock out mutants indicating the involvement of the LjNRT2.3 gene in the root nitrate acquisition and lateral root elongation pathways occurring in response to N starvation conditions. We also report an epistatic relationship between LjNRT2.3 and LjNRT2.1 suggesting a combined mode of action of these two genes in order to optimize the Lotus response to a prolonged N starvation.
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12
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Root nitrate uptake in sugarcane (Saccharum spp.) is modulated by transcriptional and presumably posttranscriptional regulation of the NRT2.1/NRT3.1 transport system. Mol Genet Genomics 2022; 297:1403-1421. [PMID: 35879567 DOI: 10.1007/s00438-022-01929-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 07/09/2022] [Indexed: 10/16/2022]
Abstract
KEY MESSAGE Nitrate uptake in sugarcane roots is regulated at the transcriptional and posttranscriptional levels based on the physiological status of the plant and is likely a determinant mechanism for discrimination against nitrate. Sugarcane (Saccharum spp.) is one of the most suitable energy crops for biofuel feedstock, but the reduced recovery of nitrogen (N) fertilizer by sugarcane roots increases the crop carbon footprint. The low nitrogen use efficiency (NUE) of sugarcane has been associated with the significantly low nitrate uptake, which limits the utilization of the large amount of nitrate available in agricultural soils. To understand the regulation of nitrate uptake in sugarcane roots, we identified the major canonical nitrate transporter genes (NRTs-NITRATE TRANSPORTERS) and then determined their expression profiles in roots under contrasting N conditions. Correlation of gene expression with 15N-nitrate uptake revealed that under N deprivation or inorganic N (ammonium or nitrate) supply in N-sufficient roots, the regulation of ScNRT2.1 and ScNRT3.1 expression is the predominant mechanism for the modulation of the activity of the nitrate high-affinity transport system. Conversely, in N-deficient roots, the induction of ScNRT2.1 and ScNRT3.1 transcription is not correlated with the marked repression of nitrate uptake in response to nitrate resupply or high N provision, which suggested the existence of a posttranscriptional regulatory mechanism. Our findings suggested that high-affinity nitrate uptake is regulated at the transcriptional and presumably at the posttranscriptional levels based on the physiological N status and that the regulation of NRT2.1 and NRT3.1 activity is likely a determinant mechanism for the discrimination against nitrate uptake observed in sugarcane roots, which contributes to the low NUE in this crop species.
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13
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Akbudak MA, Filiz E, Çetin D. Genome-wide identification and characterization of high-affinity nitrate transporter 2 (NRT2) gene family in tomato (Solanum lycopersicum) and their transcriptional responses to drought and salinity stresses. JOURNAL OF PLANT PHYSIOLOGY 2022; 272:153684. [PMID: 35349936 DOI: 10.1016/j.jplph.2022.153684] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 03/15/2022] [Accepted: 03/19/2022] [Indexed: 06/14/2023]
Abstract
The high-affinity nitrate transporter 2 (NRT2) proteins play vital roles in both nitrate (NO3-) uptake and translocation in plants. Although the gene families coding the NRT2 proteins have been identified and functionally characterized in many plant species, the systematic identification of NRT2 gene family members has not previously been reported in tomato (Solanum lycopersicum). Moreover, little is known about their expression profiles in response to different environmental stresses. The present study sought to identify the NRT2 gene family members within the tomato genome, and then to characterize them in detail by means of bioinformatics, physiological and expression analyses. Four novel NRT2 genes were identified in the tomato genome, all of which contained the same domain belonging to the major facilitator superfamily (PF07690). The co-expression network of the SlNRT2 genes revealed that they were co-expressed with several other genes in a number of different molecular pathways, including the transport, photosynthesis, fatty acid metabolism and amino acid catabolism pathways. Several phosphorylation sites were predicted in the NRT2 proteins. The SlNRT2 genes interact with many other genes that perform various functions in many crucial pathways within the tomato genome. The sequence variations observed at the gene and protein levels indicate the dynamic regulation of the SlNRT2 gene family members in relation to cell metabolism, particularly with regard to the nitrogen assimilation pathway. The responses of the SlNRT2 genes to drought and salinity stresses are diverse, and they are neither stress- nor tissue-specific. The findings of this study should provide a useful scientific basis for future studies concerning the roles of the NRT2 gene family in plants.
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Affiliation(s)
- M Aydın Akbudak
- Akdeniz University, Department of Agricultural Biotechnology, Antalya, Turkey.
| | - Ertugrul Filiz
- Duzce University, Department of Crop and Animal Production, Cilimli Vocational School, 81750, Cilimli, Duzce, Turkey.
| | - Durmuş Çetin
- Akdeniz University, Department of Agricultural Biotechnology, Antalya, Turkey
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14
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Genome-Wide Characterization of High-Affinity Nitrate Transporter 2 (NRT2) Gene Family in Brassica napus. Int J Mol Sci 2022; 23:ijms23094965. [PMID: 35563356 PMCID: PMC9104966 DOI: 10.3390/ijms23094965] [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: 04/07/2022] [Revised: 04/25/2022] [Accepted: 04/28/2022] [Indexed: 12/04/2022] Open
Abstract
Nitrate transporter 2 (NRT2) plays an essential role in Nitrogen (N) uptake, transport, utilization, and stress resistance. In this study, the NRT2 gene family in two sequenced Brassica napus ecotypes were identified, including 31 genes in ‘Zhongshuang11’ (BnaZSNRT2s) and 19 in ‘Darmor-bzh’ (BnaDarNRT2s). The candidate genes were divided into three groups (Group I−III) based on phylogenetic analyses, supported by a conserved intron-exon structure in each group. Collinearity analysis revealed that the large expansion of BnaZSNRT2s attributed to allopolyploidization of ancestors Brassica rapa and Brassica oleracea, and small-scale duplication events in B. napus. Transcription factor (TF) binding site prediction, cis-element analysis, and microRNA prediction suggested that the expressions of BnaZSNRT2s are regulated by multiple factors, and the regulatory pattern is relatively conserved in each group and is tightly connected between groups. Expression assay showed the diverse and differentiated spatial-temporal expression profiles of BnaZSNRT2s in Group I, but conserved patterns were observed in Group II/III; and the low nitrogen (LN) stress up-regulated expression profiles were presented in Group I−III, based on RNA-seq data. RT-qPCR analyses confirmed that BnaZSNRT2.5A-1 and BnaZSNRT2.5C-1 in Group II were highly up-regulated under LN stress in B. napus roots. Our results offer valid information and candidates for further functional BnaZSNRT2s studies.
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Genome-wide identification of nitrate transporter 2 (NRT2) gene family and functional analysis of MeNRT2.2 in cassava (Manihot esculenta Crantz). Gene 2022; 809:146038. [PMID: 34688819 DOI: 10.1016/j.gene.2021.146038] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 10/14/2021] [Accepted: 10/19/2021] [Indexed: 12/26/2022]
Abstract
Nitrate transporter 2 (NRT2) proteins play an important role in nitrate uptake and utilization in plants. The NRT2 family has been identified and functionally characterized in many plants. However, no systematic identification of NRT2 family members has been reported in cassava (Manihot esculenta Crantz). In this study, six MeNRT2 genes were identified from cassava genome and named as MeNRT2.1-2.6 according to their chromosomal locations. Phylogenetic tree showed that NRT2 proteins were divided into four main subgroups, which was further supported by their gene structure and conserved motifs. All six MeNRT2 genes are randomly distributed on 4 chromosomes (LG8, LG11, LG13, and LG17), two tandem duplicated genes (MeNRT2.3/MeNRT2.4) and a pair of segmental duplicated gene (MeNRT2.1/MeNRT2.2) was detected. Subsequently, expression profiles of MeNRT2 genes in eight different tissues and in response to nitrate deficient treatment were analyzed. The results showed that the MeNRT2 genes had differential expression patterns. All of MeNRT2 genes induced by nitrate deficiency, of them the MeNRT2.2 had the highest expression level after treatment. Arabidopis transformed with MeNRT2.2 gene showed higher fresh weight than wild type plants in response to N starvation, suggesting that MeNRT2.2 play important role in adapting to low nitrogen. Taken together, our results provide the reference for further analyses of the molecular functions of the MeNRT2 gene family, but also some candidate genes for developing nitrogen efficient crops.
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16
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Souza AFF, Bucher CA, Arruda LN, Rangel RP, Santos LA, Fernandes MS, Souza SR. Knockdown of OsNRT2.4 modulates root morphology and alters nitrogen metabolism in response to low nitrate availability in rice. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:5. [PMID: 37309484 PMCID: PMC10248605 DOI: 10.1007/s11032-021-01273-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 12/26/2021] [Indexed: 06/14/2023]
Abstract
The expression patterns of the NRT2 genes have been well described; however, the role of OsNRT2.4 in root growth is not well known. In this study, we thus aimed at investigating the role of high-affinity NO3- transport OsNRT2.4 in root growth modulation. Through the amiRNA-mediated gene silencing technique, we successfully obtained osnrt2.4 knockdown lines to study the role of OsNRT2.4 on root growth under low nitrate conditions. We performed real-time PCR analysis to investigate the relative gene expression level in root and shoot, soluble metabolites, and measurement of root system. Knockdown of OsNRT2.4 decreased rice growth. The comparison with wild-type (WT) plants showed that (i) knockdown of OsNRT2.4 inhibited root formation under low NO3- supply; (ii) we demonstrated that the mutant lines had significantly increased NO3- uptake than WT plants when grown in different nitrate supplies; (iii) osnrt2.4 knockdown lines showed an alteration in nitrogen metabolism, and this affected the root growth; and (iv) the downregulation of OsNRT2.4 enhanced the expression of gene response of low external NO3- concentrations. Herein we provide new insights in OsNRT2.4 functions. Our data demonstrated that OsNRT2.4 plays a role in root growth, nitrogen metabolic pathway and probably have functions in nitrate transport from root to shoot under low nitrate availability in rice. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-021-01273-6.
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Affiliation(s)
- Andressa Fabiane Faria Souza
- Department of Soil, Plant Nutrition Group, Federal Rural University of Rio de Janeiro (UFRRJ), Rodovia BR 465 km 7, Seropédica, RJ 23890-000 Brazil
| | - Carlos Alberto Bucher
- Department of Soil, Plant Nutrition Group, Federal Rural University of Rio de Janeiro (UFRRJ), Rodovia BR 465 km 7, Seropédica, RJ 23890-000 Brazil
| | - Leilson Novaes Arruda
- Department of Soil, Plant Nutrition Group, Federal Rural University of Rio de Janeiro (UFRRJ), Rodovia BR 465 km 7, Seropédica, RJ 23890-000 Brazil
| | - Rafael Passos Rangel
- Department of Soil, Plant Nutrition Group, Federal Rural University of Rio de Janeiro (UFRRJ), Rodovia BR 465 km 7, Seropédica, RJ 23890-000 Brazil
| | - Leandro Azevedo Santos
- Department of Soil, Plant Nutrition Group, Federal Rural University of Rio de Janeiro (UFRRJ), Rodovia BR 465 km 7, Seropédica, RJ 23890-000 Brazil
| | - Manlio Silvestre Fernandes
- Department of Soil, Plant Nutrition Group, Federal Rural University of Rio de Janeiro (UFRRJ), Rodovia BR 465 km 7, Seropédica, RJ 23890-000 Brazil
| | - Sonia Regina Souza
- Department of Chemistry, Plant Biochemistry Group, Federal Rural University of Rio de Janeiro (UFRRJ), Rodovia BR 465 km 7, Seropédica, RJ 23890-000 Brazil
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Fiaz S, Wang X, Khan SA, Ahmar S, Noor MA, Riaz A, Ali K, Abbas F, Mora-Poblete F, Figueroa CR, Alharthi B. Novel plant breeding techniques to advance nitrogen use efficiency in rice: A review. GM CROPS & FOOD 2021; 12:627-646. [PMID: 34034628 PMCID: PMC9208628 DOI: 10.1080/21645698.2021.1921545] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Recently, there has been a remarkable increase in rice production owing to genetic improvement and increase in application of synthetic fertilizers. For sustainable agriculture, there is dire need to maintain a balance between profitability and input cost. To meet the steady growing demands of the farming community, researchers are utilizing all available resources to identify nutrient use efficient germplasm, but with very little success. Therefore, it is essential to understand the underlying genetic mechanism controlling nutrients efficiency, with the nitrogen use efficiency (NUE) being the most important trait. Information regarding genetic factors controlling nitrogen (N) transporters, assimilators, and remobilizers can help to identify candidate germplasms via high-throughput technologies. Large-scale field trials have provided morphological, physiological, and biochemical trait data for the detection of genomic regions controlling NUE. The functional aspects of these attributes are time-consuming, costly, labor-intensive, and less accurate. Therefore, the application of novel plant breeding techniques (NPBTs) with context to genome engineering has opened new avenues of research for crop improvement programs. Most recently, genome editing technologies (GETs) have undergone enormous development with various versions from Cas9, Cpf1, base, and prime editing. These GETs have been vigorously adapted in plant sciences for novel trait development to insure food quantity and quality. Base editing has been successfully applied to improve NUE in rice, demonstrating the potential of GETs to develop germplasms with improved resource use efficiency. NPBTs continue to face regulatory setbacks in some countries due to genome editing being categorized in the same category as genetically modified (GM) crops. Therefore, it is essential to involve all stakeholders in a detailed discussion on NPBTs and to formulate uniform policies tackling biosafety, social, ethical, and environmental concerns. In the current review, we have discussed the genetic mechanism of NUE and NPBTs for crop improvement programs with proof of concepts, transgenic and GET application for the development of NUE germplasms, and regulatory aspects of genome edited crops with future directions considering NUE.
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Affiliation(s)
- Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur 22620, Khyber, Pakhtunkhwa, Pakistan
| | - Xiukang Wang
- College of Life Sciences, Yan'an University, Yan'an, Shaanxi, China
| | - Sher Aslam Khan
- Department of Plant Breeding and Genetics, The University of Haripur 22620, Khyber, Pakhtunkhwa, Pakistan
| | - Sunny Ahmar
- Institute of Biological Sciences, Campus Talca, Universidad deTalca, Talca, Chile
| | - Mehmood Ali Noor
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Key Laboratory of Crop Physiology and Ecology, Ministry of Agriculture, Beijing, China
| | - Aamir Riaz
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang, China
| | - Kazim Ali
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Islamabad, Pakistan
| | - Farhat Abbas
- Research Center for Ornamental Plants, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Freddy Mora-Poblete
- Institute of Biological Sciences, Campus Talca, Universidad deTalca, Talca, Chile
| | - Carlos R Figueroa
- Institute of Biological Sciences, Campus Talca, Universidad deTalca, Talca, Chile
| | - Badr Alharthi
- College of Khurma, Taif University, Taif, Saudi Arabia.,College of Science and Engineering, Flinders University, Adelaide, South Australia
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Physiological and Molecular Traits Associated with Nitrogen Uptake under Limited Nitrogen in Soft Red Winter Wheat. PLANTS 2021; 10:plants10010165. [PMID: 33477261 PMCID: PMC7830070 DOI: 10.3390/plants10010165] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/09/2021] [Accepted: 01/14/2021] [Indexed: 11/17/2022]
Abstract
A sufficient nitrogen (N) supply is pivotal for high grain yield and desired grain protein content in wheat (Triticum aestivum L.). Elucidation of physiological and molecular mechanisms underlying nitrogen use efficiency (NUE) will enhance our ability to develop new N-saving varieties in wheat. In this study, we analyzed two soft red winter wheat genotypes, VA08MAS-369 and VA07W-415, with contrasting NUE under limited N. Our previous study demonstrated that higher NUE in VA08MAS-369 resulted from accelerated senescence and N remobilization in flag leaves at low N. The present study revealed that VA08MAS-369 also exhibited higher nitrogen uptake efficiency (NUpE) than VA07W-415 under limited N. VA08MAS-369 consistently maintained root growth parameters such as maximum root depth, total root diameter, total root surface area, and total root volume under N limitation, relative to VA07W-415. Our time-course N content analysis indicated that VA08MAS-369 absorbed N more abundantly than VA07W-415 after the anthesis stage at low N. More efficient N uptake in VA08MAS-369 was associated with the increased expression of genes encoding a two-component high-affinity nitrate transport system, including four NRT2s and three NAR2s, in roots at low N. Altogether, these results demonstrate that VA08MAS-369 can absorb N efficiently even under limited N due to maintained root development and increased function of N uptake. The ability of VA08MAS-369 in N remobilization and uptake suggests that this genotype could be a valuable genetic material for the improvement of NUE in soft red winter wheat.
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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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20
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Tong J, Walk TC, Han P, Chen L, Shen X, Li Y, Gu C, Xie L, Hu X, Liao X, Qin L. Genome-wide identification and analysis of high-affinity nitrate transporter 2 (NRT2) family genes in rapeseed (Brassica napus L.) and their responses to various stresses. BMC PLANT BIOLOGY 2020; 20:464. [PMID: 33036562 PMCID: PMC7547492 DOI: 10.1186/s12870-020-02648-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 09/14/2020] [Indexed: 05/22/2023]
Abstract
BACKGROUND High-affinity nitrate transporter 2 (NRT2) genes have been implicated in nitrate absorption and remobilization under nitrogen (N) starvation stress in many plant species, yet little is known about this gene family respond to various stresses often occurs in the production of rapeseed (Brassica napus L.). RESULTS This report details identification of 17 NRT2 gene family members in rapeseed, as well as, assessment of their expression profiles using RNA-seq analysis and qRT-PCR assays. In this study, all BnNRT2.1 members, BnNRT2.2a and BnNRT2.4a were specifically expressed in root tissues, while BnNRT2.7a and BnNRT2.7b were mainly expressed in aerial parts, including as the predominantly expressed NRT2 genes detected in seeds. This pattern of shoot NRT expression, along with homology to an Arabidopsis NRT expressed in seeds, strongly suggests that both BnNRT2.7 genes play roles in seed nitrate accumulation. Another rapeseed NRT, BnNRT2.5 s, exhibited intermediate expression, with transcripts detected in both shoot and root tissues. Functionality of BnNRT2s genes was further outlined by testing for adaptive responses in expression to exposure to a series of environmental stresses, including N, phosphorus (P) or potassium (K) deficiency, waterlogging and drought. In these tests, most NRT2 gene members were up-regulated by N starvation and restricted by the other stresses tested herein. In contrast to this overall trend, transcription of BnNRT2.1a was up-regulated under waterlogging and K deficiency stress, and BnNRT2.5 s was up-regulated in roots subjected to waterlogging. Furthermore, the mRNA levels of BnNRT2.7 s were enhanced under both waterlogging stress and P or K deficiency conditions. These results suggest that these three BnNRT2 genes might participate in crosstalk among different stress response pathways. CONCLUSIONS The results presented here outline a diverse set of NRT2 genes present in the rapeseed genome that collectively carry out specific functions throughout rapeseed development, while also responding not just to N deficiency, but also to several other stresses. Targeting of individual BnNRT2 members that coordinate rapeseed nitrate uptake and transport in response to cues from multiple stress response pathways could significantly expand the genetic resources available for improving rapeseed resistance to environmental stresses.
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Affiliation(s)
- Jiafeng Tong
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetics Improvement of Oil Crops of the Ministry of Agriculture and Rural Affairs, Wuhan, 430062, P. R. China
| | | | - Peipei Han
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetics Improvement of Oil Crops of the Ministry of Agriculture and Rural Affairs, Wuhan, 430062, P. R. China
- Institute of Agriculture Science in Jiangsu Coastal Area, Yancheng, 224002, P. R. China
| | - Liyu Chen
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, P. R. China
| | - Xinjie Shen
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetics Improvement of Oil Crops of the Ministry of Agriculture and Rural Affairs, Wuhan, 430062, P. R. China
| | - Yinshui Li
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetics Improvement of Oil Crops of the Ministry of Agriculture and Rural Affairs, Wuhan, 430062, P. R. China
| | - Chiming Gu
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetics Improvement of Oil Crops of the Ministry of Agriculture and Rural Affairs, Wuhan, 430062, P. R. China
| | - Lihua Xie
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetics Improvement of Oil Crops of the Ministry of Agriculture and Rural Affairs, Wuhan, 430062, P. R. China
| | - Xiaojia Hu
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetics Improvement of Oil Crops of the Ministry of Agriculture and Rural Affairs, Wuhan, 430062, P. R. China
| | - Xing Liao
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetics Improvement of Oil Crops of the Ministry of Agriculture and Rural Affairs, Wuhan, 430062, P. R. China.
| | - Lu Qin
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetics Improvement of Oil Crops of the Ministry of Agriculture and Rural Affairs, Wuhan, 430062, P. R. China.
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21
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Valkov VT, Sol S, Rogato A, Chiurazzi M. The functional characterization of LjNRT2.4 indicates a novel, positive role of nitrate for an efficient nodule N 2 -fixation activity. THE NEW PHYTOLOGIST 2020; 228:682-696. [PMID: 32542646 DOI: 10.1111/nph.16728] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 05/27/2020] [Indexed: 05/25/2023]
Abstract
Atmospheric nitrogen (N2) -fixing nodules are formed on the roots of legume plants as result of the symbiotic interaction with rhizobia. Nodule functioning requires high amounts of carbon and energy, and therefore legumes have developed finely tuned mechanisms to cope with changing external environmental conditions, including nutrient availability and flooding. The investigation of the role of nitrate as regulator of the symbiotic N2 fixation has been limited to the inhibitory effects exerted by high external concentrations on nodule formation, development and functioning. We describe a nitrate-dependent route acting at low external concentrations that become crucial in hydroponic conditions to ensure an efficient nodule functionality. Combined genetic, biochemical and molecular studies are used to unravel the novel function of the LjNRT2.4 gene. Two independent null mutants are affected by the nitrate content of nodules, consistent with LjNRT2.4 temporal and spatial profiles of expression. The reduced nodular nitrate content is associated to a strong reduction of nitrogenase activity and a severe N-starvation phenotype observed under hydroponic conditions. We also report the effects of the mutations on the nodular nitric oxide (NO) production and content. We discuss the involvement of LjNRT2.4 in a nitrate-NO respiratory chain taking place in the N2 -fixing nodules.
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Affiliation(s)
- Vladimir Totev Valkov
- Institute of Biosciences and Bioresources, IBBR, CNR, Via P. Castellino 111, Napoli, 80131, Italy
| | - Stefano Sol
- Institute of Biosciences and Bioresources, IBBR, CNR, Via P. Castellino 111, Napoli, 80131, Italy
| | - Alessandra Rogato
- Institute of Biosciences and Bioresources, IBBR, CNR, Via P. Castellino 111, Napoli, 80131, Italy
| | - Maurizio Chiurazzi
- Institute of Biosciences and Bioresources, IBBR, CNR, Via P. Castellino 111, Napoli, 80131, Italy
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22
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Han X, Wu K, Fu X, Liu Q. Improving coordination of plant growth and nitrogen metabolism for sustainable agriculture. ABIOTECH 2020; 1:255-275. [PMID: 36304130 PMCID: PMC9590520 DOI: 10.1007/s42994-020-00027-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 07/20/2020] [Indexed: 01/25/2023]
Abstract
The agricultural green revolution of the 1960s boosted cereal crop yield was in part due to cultivation of semi-dwarf green revolution varieties. The semi-dwarf plants resist lodging and require high nitrogen (N) fertilizer inputs to maximize yield. To produce higher grain yield, inorganic fertilizer has been overused by Chinese farmers in intensive crop production. With the ongoing increase in the food demand of global population and the environmental pollution, improving crop productivity with reduced N supply is a pressing challenge. Despite a great deal of research efforts, to date only a few genes that improve N use efficiency (NUE) have been identified. The molecular mechanisms underlying the coordination of plant growth, carbon (C) and N assimilation is still not fully understood, thus preventing significant improvement. Recent advances have shed light on how explore NUE within an overall plant biology system that considered the co-regulation of plant growth, C and N metabolisms as a whole, rather than focusing specifically on N uptake and assimilation. There are several potential approaches to improve NUE discussed in this review. Increasing knowledge of how plants sense and respond to changes in N availability, as well as identifying new targets for breeding strategies to simultaneously improve NUE and grain yield, could usher in a new green revolution.
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Affiliation(s)
- Xiang Han
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101 China
| | - Kun Wu
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101 China
| | - Xiangdong Fu
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101 China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Qian Liu
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101 China
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23
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Thi Nong H, Tateishi R, Suriyasak C, Kobayashi T, Oyama Y, Chen WJ, Matsumoto R, Hamaoka N, Iwaya-Inoue M, Ishibashi Y. Effect of Seedling Nitrogen Condition on Subsequent Vegetative Growth Stages and Its Relationship to the Expression of Nitrogen Transporter Genes in Rice. PLANTS (BASEL, SWITZERLAND) 2020; 9:E861. [PMID: 32646051 PMCID: PMC7412562 DOI: 10.3390/plants9070861] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 06/23/2020] [Accepted: 07/03/2020] [Indexed: 11/17/2022]
Abstract
Nitrogen (N) deficiency is one of the most common problems in soils, limiting crop growth and production. However, the effects of N limitation in seedlings on vegetative growth remain poorly understood. Here, we show that N limitation in rice seedlings restricted vegetative growth but not yield. Aboveground parts were affected mainly during the period of tillering, but belowground parts were sensitive throughout vegetative growth, especially during panicle development. At the tillering stage, N-limited plants had a significantly lower N content in shoots, but not in roots. On the other hand, N content in roots during the panicle development stage was significantly lower in N-limited plants. This distinct response was driven by significant changes in expression of N transporter genes during growth. Under N limitation, N translocation from roots to shoots was greatly sped up by systemic expression of N transporter genes to obtain balanced growth. N limitation during the seedling stage did not reduce any yield components. We conclude that the N condition during the seedling stage affects physiological responses such as N translocation through the expression of N transporter genes.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Yushi Ishibashi
- Graduate school of Bioresource and Bioenviromental Sciences, Kyushu University, Mootoka 774, Fukuoka 819–0395, Japan; (H.T.N.); (R.T.); (C.S.); (T.K.); (Y.O.); (W.J.C.); (R.M.); (N.H.); (M.I.-I.)
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24
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Lou D, Chen Z, Yu D, Yang X. SAPK2 contributes to rice yield by modulating nitrogen metabolic processes under reproductive stage drought stress. RICE (NEW YORK, N.Y.) 2020; 13:35. [PMID: 32514747 PMCID: PMC7280414 DOI: 10.1186/s12284-020-00395-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 05/25/2020] [Indexed: 05/11/2023]
Abstract
BACKGROUND The sucrose non-fermenting 1-related kinases 2 (SnRK2s) play important roles in osmotic stress responses in A. thaliana and rice (Oryza sativa L.). Osmotic stress/ABA-activated protein kinase 2 (SAPK2) is a member of SnRK2s subclass II in rice, but its function in rice yield under drought stress is unclear. RESULTS Compared with wild-type (Oryza.Sativa L.spp.japonica, WT) plants, the sapk2 rice mutant lines were shorter and produced fewer grains per panicle, smaller grains and lower grain yield under reproductive stage drought stress (RDS). Subsequent analysis suggested that SAPK2 considerably influences the nitrogen, phosphorus, and potassium contents of rice grains. The examination of rice seedling growth and development under nutrient-deprived conditions (-N, -K, and - P) proved that SAPK2 can significantly affect rice seedling growth and root development in hydroponic cultures lacking N and K. Moreover, the NO3- influx rate and nitrate concentration analysis indicated that SAPK2 promotes nitrate uptake and assimilation by regulating nitrate-related transporters. CONCLUSION These results suggest that SAPK2 could enhance grain production by regulating nitrogen utilization efficiency under RDS. Our work provided insights to breeding drought tolerant rice with high nutrient uptake.
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Affiliation(s)
- Dengji Lou
- School of Chemical, Biological and Environmental Sciences, Yuxi Normal University, Yuxi, 653100, China
| | - Zhen Chen
- School of Chemical, Biological and Environmental Sciences, Yuxi Normal University, Yuxi, 653100, China
| | - Diqiu Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, China.
| | - Xiaoyan Yang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, Yunnan, China.
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25
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Yang X, Xia X, Zeng Y, Nong B, Zhang Z, Wu Y, Tian Q, Zeng W, Gao J, Zhou W, Liang H, Li D, Deng G. Genome-wide identification of the peptide transporter family in rice and analysis of the PTR expression modulation in two near-isogenic lines with different nitrogen use efficiency. BMC PLANT BIOLOGY 2020; 20:193. [PMID: 32375632 PMCID: PMC7203820 DOI: 10.1186/s12870-020-02419-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 04/29/2020] [Indexed: 05/18/2023]
Abstract
BACKGROUND Nitrogen (N) is a major nutrient element for crop growth. In plants, the members of the peptide transporter (PTR) gene family may involve in nitrate uptake and transport. Here, we identified PTR gene family in rice and analyzed their expression profile in near-isogenic lines. RESULTS We identified 96, 85 and 78 PTR genes in Nipponbare, R498 and Oryza glaberrima, and the phylogenetic trees were similar in Asian cultivated rice and African cultivated rice. The number of PTR genes was higher in peanut (125) and soybean (127). The 521 PTR genes in rice, maize, sorghum, peanut, soybean and Arabidopsis could be classified into 4 groups, and their distribution was different between monocots and dicots. In Nipponbare genome, the 25 PTR genes were distributed in 5 segmental duplication regions on chromosome 1, 2, 3, 4, 5, 7, 8, 9, and 10. The PTR genes in rice have 0-11 introns and 1-12 exons, and 16 of them have the NPF (NRT1/PTR family) domain. The results of RNA-seq showed that the number of differentially expressed genes (DEGs) between NIL15 and NIL19 at three stages were 928, 1467, and 1586, respectively. Under low N conditions, the number of differentially expressed PTR genes increased significantly. The RNA-seq data was analyzed using WGCNA to predict the potential interaction between genes. We classified the genes with similar expression pattern into one module, and obtained 25 target modules. Among these modules, three modules may be involved in rice N uptake and utilization, especially the brown module, in which hub genes were annotated as protein kinase that may regulate rice N metabolism. CONCLUSIONS In this study, we comprehensively analyzed the PTR gene family in rice. 96 PTR genes were identified in Nippobare genome and 25 of them were located on five large segmental duplication regions. The Ka/Ks ratio indicated that many PTR genes had undergone positive selection. The RNA-seq results showed that many PTR genes were involved in rice nitrogen use efficiency (NUE), and protein kinases might play an important role in this process. These results provide a fundamental basis to improve the rice NUE via molecular breeding.
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Affiliation(s)
- Xinghai Yang
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, 174 East Daxue Road, Nanning, 530007, Guangxi, China.
| | - Xiuzhong Xia
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, 174 East Daxue Road, Nanning, 530007, Guangxi, China
| | - Yu Zeng
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, 174 East Daxue Road, Nanning, 530007, Guangxi, China
| | - Baoxuan Nong
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, 174 East Daxue Road, Nanning, 530007, Guangxi, China
| | - Zongqiong Zhang
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, 174 East Daxue Road, Nanning, 530007, Guangxi, China
| | - Yanyan Wu
- Biotechnology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China
| | - Qinglan Tian
- Biotechnology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China
| | - Weiying Zeng
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China
| | - Ju Gao
- Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China
| | - Weiyong Zhou
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, 174 East Daxue Road, Nanning, 530007, Guangxi, China
| | - Haifu Liang
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, 174 East Daxue Road, Nanning, 530007, Guangxi, China
| | - Danting Li
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, 174 East Daxue Road, Nanning, 530007, Guangxi, China.
| | - Guofu Deng
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, 174 East Daxue Road, Nanning, 530007, Guangxi, China.
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26
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Guo B, Li Y, Wang S, Li D, Lv C, Xu R. Characterization of the Nitrate Transporter gene family and functional identification of HvNRT2.1 in barley (Hordeum vulgare L.). PLoS One 2020; 15:e0232056. [PMID: 32324773 PMCID: PMC7179922 DOI: 10.1371/journal.pone.0232056] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 04/06/2020] [Indexed: 11/19/2022] Open
Abstract
Nitrogen use efficiency (NUE) is the efficiency with which plants acquire and use nitrogen. Plants have high-affinity nitrate transport systems, which involve certain nitrate transporter (NRT) genes. However, limited data are available on the contribution of the NRT2/3 gene family in barley nitrate transport. In the present study, ten putative NRT2 and three putative NRT3 genes were identified using bioinformatics methods. All the HvNRT2/3 genes were located on chromosomes 3H, 5H, 6H or 7H. Remarkably, the presence of tandem repeats indicated that duplication events contributed to the expansion of the NRT2 gene family in barley. In addition, the HvNRT2/3 genes displayed various expression patterns at selected developmental stages and were induced in the roots by both low and high nitrogen levels. Furthermore, the overexpression of HvNRT2.1 improved the yield related traits in Arabidopsis. Taken together, the data generated in the present study will be useful for genome-wide analyses to determine the precise role of the HvNRT2/3 genes during barley development, with the ultimate goal of improving NUE and crop production.
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Affiliation(s)
- Baojian Guo
- Jiangsu Key Laboratory of Crop Genetics and Physiology/ Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
- Barley Research Institution of Yangzhou University, Yangzhou University, Yangzhou, China
| | - Ying Li
- Jiangsu Key Laboratory of Crop Genetics and Physiology/ Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
- Barley Research Institution of Yangzhou University, Yangzhou University, Yangzhou, China
| | - Shuang Wang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/ Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
- Barley Research Institution of Yangzhou University, Yangzhou University, Yangzhou, China
| | - Dongfang Li
- Jiangsu Key Laboratory of Crop Genetics and Physiology/ Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
- Barley Research Institution of Yangzhou University, Yangzhou University, Yangzhou, China
| | - Chao Lv
- Jiangsu Key Laboratory of Crop Genetics and Physiology/ Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
- Barley Research Institution of Yangzhou University, Yangzhou University, Yangzhou, China
| | - Rugen Xu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/ Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
- Barley Research Institution of Yangzhou University, Yangzhou University, Yangzhou, China
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27
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Mauceri A, Bassolino L, Lupini A, Badeck F, Rizza F, Schiavi M, Toppino L, Abenavoli MR, Rotino GL, Sunseri F. Genetic variation in eggplant for Nitrogen Use Efficiency under contrasting NO 3 - supply. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2020; 62:487-508. [PMID: 31087763 DOI: 10.1111/jipb.12823] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 05/08/2019] [Indexed: 05/03/2023]
Abstract
Eggplant (Solanum melongena L.) yield is highly sensitive to N fertilization, the excessive use of which is responsible for environmental and human health damage. Lowering N input together with the selection of improved Nitrogen-Use-Efficiency (NUE) genotypes, more able to uptake, utilize, and remobilize N available in soils, can be challenging to maintain high crop yields in a sustainable agriculture. The aim of this study was to explore the natural variation among eggplant accessions from different origins, in response to Low (LN) and High (HN) Nitrate (NO3 - ) supply, to identify NUE-contrasting genotypes and their NUE-related traits, in hydroponic and greenhouse pot experiments. Two eggplants, AM222 and AM22, were identified as N-use efficient and inefficient, respectively, in hydroponic, and these results were confirmed in a pot experiment, when crop yield was also evaluated. Overall, our results indicated the key role of N-utilization component (NUtE) to confer high NUE. The remobilization of N from leaves to fruits may be a strategy to enhance NUtE, suggesting glutamate synthase as a key enzyme. Further, omics technologies will be used for focusing on C-N metabolism interacting networks. The availability of RILs from two other selected NUE-contrasting genotypes will allow us to detect major genes/quantitative trait loci related to NUE.
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Affiliation(s)
- Antonio Mauceri
- Dipartimento Agraria, Università degli Studi Mediterranea di Reggio Calabria, I-89124, Reggio Calabria, Italy
| | - Laura Bassolino
- CREA Centro di ricerca Genomica e Bioinformatica, I-26836, Montanaso Lombardo, Italy
| | - Antonio Lupini
- Dipartimento Agraria, Università degli Studi Mediterranea di Reggio Calabria, I-89124, Reggio Calabria, Italy
| | - Franz Badeck
- CREA Centro di ricerca Genomica e Bioinformatica, I-29017, Fiorenzuola d'Arda, Italy
| | - Fulvia Rizza
- CREA Centro di ricerca Genomica e Bioinformatica, I-29017, Fiorenzuola d'Arda, Italy
| | - Massimo Schiavi
- CREA Centro di ricerca Genomica e Bioinformatica, I-26836, Montanaso Lombardo, Italy
| | - Laura Toppino
- CREA Centro di ricerca Genomica e Bioinformatica, I-26836, Montanaso Lombardo, Italy
| | - Maria Rosa Abenavoli
- Dipartimento Agraria, Università degli Studi Mediterranea di Reggio Calabria, I-89124, Reggio Calabria, Italy
| | - Giuseppe L Rotino
- CREA Centro di ricerca Genomica e Bioinformatica, I-26836, Montanaso Lombardo, Italy
| | - Francesco Sunseri
- Dipartimento Agraria, Università degli Studi Mediterranea di Reggio Calabria, I-89124, Reggio Calabria, Italy
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28
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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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29
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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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31
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Aseel DG, Mostafa Y, Riad SA, Hafez EE. Improvement of nitrogen use efficiency in maize using molecular and physiological approaches. Symbiosis 2019. [DOI: 10.1007/s13199-019-00616-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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32
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Wang J, Hüner N, Tian L. Identification and molecular characterization of the Brachypodium distachyon NRT2 family, with a major role of BdNRT2.1. PHYSIOLOGIA PLANTARUM 2019; 165:498-510. [PMID: 29498420 DOI: 10.1111/ppl.12716] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 02/09/2018] [Accepted: 02/27/2018] [Indexed: 05/28/2023]
Abstract
The small monocot plant Brachypodium distachyon is rapidly emerging as a powerful model system to study questions unique to the monocot crops. An extensive BLAST search was carried to identify putative orthologues of the Arabidopsis NRT2 genes in the fully sequenced Brachypodium genome. Seven genes encoding putative high-affinity nitrate transporters (BdNRT2) were identified. Transcriptional analysis of individual BdNRT2 gene under various nitrogen sources and levels in the wild-type and a T-DNA mutant of BdNRT2.1 were performed. A transgenic approach was taken to complement the bdnrt2.1 mutant. BdNRT2.1 and BdNRT2.2 were strongly induced by nitrate resupply to nitrogen-starved plants and were classified as inducible genes. BdNRT2.5 was found to be repressed by nitrate resupply whereas other members were constitutively expressed in the root. Interestingly, higher ammonium concentrations also triggered similar gene expression regulation, suggesting BdNRT2 gene expression was also governed by internal nitrogen status, not just external nitrate concentrations. In bdnrt2.1 mutant, the high-affinity transporter system (HATS) was reduced by 30% and BdNRT2.2 and BdNRT2.6 were differentially regulated. This pioneering research demonstrates that genes in the BdNRT2 family have diverse roles, differing from the Arabidopsis AtNRT2 family, in response to various nitrogen conditions. BdNRT2.1 serves as a key member of the family.
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Affiliation(s)
- Jiang Wang
- Department of Biology, University of Western Ontario, London, Ontario, Canada
| | - Norman Hüner
- Department of Biology, University of Western Ontario, London, Ontario, Canada
| | - Lining Tian
- Department of Biology, University of Western Ontario, London, Ontario, Canada
- London Research and Development Center, Agriculture and Agri-Food Canada, London, Ontario, Canada
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Li Y, Li J, Yan Y, Liu W, Zhang W, Gao L, Tian Y. Knock-Down of CsNRT2.1, a Cucumber Nitrate Transporter, Reduces Nitrate Uptake, Root length, and Lateral Root Number at Low External Nitrate Concentration. FRONTIERS IN PLANT SCIENCE 2018; 9:722. [PMID: 29911677 PMCID: PMC5992502 DOI: 10.3389/fpls.2018.00722] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Accepted: 05/14/2018] [Indexed: 05/08/2023]
Abstract
Nitrogen (N) is a macronutrient that plays a crucial role in plant growth and development. Nitrate ( NO 3 - ) is the most abundant N source in aerobic soils. Plants have evolved two adaptive mechanisms such as up-regulation of the high-affinity transport system (HATS) and alteration of the root system architecture (RSA), allowing them to cope with the temporal and spatial variation of NO 3 - . However, little information is available regarding the nitrate transporter in cucumber, one of the most important fruit vegetables in the world. In this study we isolated a nitrate transporter named CsNRT2.1 from cucumber. Analysis of the expression profile of the CsNRT2.1 showed that CsNRT2.1 is a high affinity nitrate transporter which mainly located in mature roots. Subcellular localization analysis revealed that CsNRT2.1 is a plasma membrane transporter. In N-starved CsNRT2.1 knock-down plants, both of the constitutive HATS (cHATS) and inducible HATS (iHATS) were impaired under low external NO 3 - concentration. Furthermore, the CsNRT2.1 knock-down plants showed reduced root length and lateral root numbers. Together, our results demonstrated that CsNRT2.1 played a dual role in regulating the HATS and RSA to acquire NO 3 - effectively under N limitation.
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Affiliation(s)
- Yang Li
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, China
| | - Juanqi Li
- College of Horticulture, Henan Agricultural University, Zhengzhou, China
| | - Yan Yan
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, China
| | - Wenqian Liu
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, China
| | - Wenna Zhang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, China
| | - Lihong Gao
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, China
| | - Yongqiang Tian
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, China
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Pellizzaro A, Alibert B, Planchet E, Limami AM, Morère-Le Paven MC. Nitrate transporters: an overview in legumes. PLANTA 2017; 246:585-595. [PMID: 28653185 DOI: 10.1007/s00425-017-2724-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 06/19/2017] [Indexed: 05/02/2023]
Abstract
The nitrate transporters, belonging to NPF and NRT2 families, play critical roles in nitrate signaling, root growth and nodule development in legumes. Nitrate plays an essential role during plant development as nutrient and also as signal molecule, in both cases working via the activity of nitrate transporters. To date, few studies on NRT2 or NPF nitrate transporters in legumes have been reported, and most of those concern Lotus japonicus and Medicago truncatula. A molecular characterization led to the identification of 4 putative LjNRT2 and 37 putative LjNPF gene sequences in L. japonicus. In M. truncatula, the NRT2 family is composed of 3 putative members. Using the new genome annotation of M. truncatula (Mt4.0), we identified, for this review, 97 putative MtNPF sequences, including 32 new sequences relative to previous studies. Functional characterization has been published for only two MtNPF genes, encoding nitrate transporters of M. truncatula. Both transporters have a role in root system development via abscisic acid signaling: MtNPF6.8 acts as a nitrate sensor during the cell elongation of the primary root, while MtNPF1.7 contributes to the cellular organization of the root tip and nodule formation. An in silico expression study of MtNPF genes confirmed that NPF genes are expressed in nodules, as previously shown for L. japonicus, suggesting a role for the corresponding proteins in nitrate transport, or signal perception in nodules. This review summarizes our knowledge of legume nitrate transporters and discusses new roles for these proteins based on recent discoveries.
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Affiliation(s)
- Anthoni Pellizzaro
- IRHS, Agrocampus Ouest, INRA, Université d'Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071, Beaucouzé Cedex, France
| | - Bénédicte Alibert
- IRHS, Agrocampus Ouest, INRA, Université d'Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071, Beaucouzé Cedex, France
| | - Elisabeth Planchet
- IRHS, Agrocampus Ouest, INRA, Université d'Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071, Beaucouzé Cedex, France
| | - Anis M Limami
- IRHS, Agrocampus Ouest, INRA, Université d'Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071, Beaucouzé Cedex, France
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Xuan W, Beeckman T, Xu G. Plant nitrogen nutrition: sensing and signaling. CURRENT OPINION IN PLANT BIOLOGY 2017; 39:57-65. [PMID: 28614749 DOI: 10.1016/j.pbi.2017.05.010] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 05/24/2017] [Accepted: 05/28/2017] [Indexed: 05/26/2023]
Abstract
In response to external fluctuations of nitrogen (N) supplies, plants can activate complex regulatory networks for optimizing N uptake and utilization. In this review, we highlight novel N-responsive sensors, transporters, and signaling molecules recently identified in the dicot Arabidopsis and the monocot rice, and discuss their potential roles in N sensing and signaling. Furthermore, over the last couple of years, N sensing has been shown to be affected by multiple external factors, which act as local signals to trigger systemic signaling coordinated by long-distance mobile signals. Understanding of this complex regulatory network provides a foundation for the development of novel strategies to increase the root N acquisition efficiency under varying N conditions for crop production.
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Affiliation(s)
- Wei Xuan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Tom Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Ghent, Belgium; VIB-UGent Center for Plant Systems Biology, Technologiepark 927, B-9052 Ghent, Belgium
| | - Guohua Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing 210095, PR China.
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Li H, Hu B, Chu C. Nitrogen use efficiency in crops: lessons from Arabidopsis and rice. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:2477-2488. [PMID: 28419301 DOI: 10.1093/jxb/erx101] [Citation(s) in RCA: 163] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Application of chemical fertilizers, especially nitrogen (N), to crops has increased dramatically in the last half century and therefore developing crop varieties with improved N use efficiency (NUE) is urgent for sustainable agriculture. N utilization procedures generally can be divided into uptake, transport, and assimilation. Transporters for nitrate or ammonium acquisition and enzymes for assimilation are among the essential components determining NUE, and many transcription factors also play a pivotal role in regulating N use-associated genes, thereby contributing to NUE. Although some efforts in improving NUE have been made in various plants, the regulatory mechanisms underlying NUE are still elusive, and NUE improvement in crop breeding is very limited. In this review, the crucial components involved in N utilization and the candidates with the potential for NUE improvement in dicot Arabidopsis and monocot rice are summarized. In addition, strategies based on new techniques which can be used for dissecting regulatory mechanisms of NUE and also the possible ways in which NUE can be improved in crops are discussed.
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Affiliation(s)
- Hua Li
- State Key Laboratory of Plant Genomics and CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Bin Hu
- State Key Laboratory of Plant Genomics and CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chengcai Chu
- State Key Laboratory of Plant Genomics and CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
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Wu Y, Yang W, Wei J, Yoon H, An G. Transcription Factor OsDOF18 Controls Ammonium Uptake by Inducing Ammonium Transporters in Rice Roots. Mol Cells 2017; 40:178-185. [PMID: 28292004 PMCID: PMC5386955 DOI: 10.14348/molcells.2017.2261] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 01/05/2017] [Accepted: 01/06/2017] [Indexed: 12/29/2022] Open
Abstract
Nitrogen is one of the most important mineral elements for plant growth. We studied the functional roles of Oryza sativa DNA BINDING WITH ONE FINGER 18 (OsDOF18) in controlling ammonium uptake. The growth of null mutants of OsDOF18 was retarded in a medium containing ammonium as the sole nitrogen source. In contrast, those mutants grew normally in a medium with nitrate as the sole nitrogen source. The gene expression was induced by ammonium but not by nitrate. Uptake of ammonium was lower in osdof18 mutants than in the wild type, while that of nitrate was not affected by the mutation. This indicated that OsDOF18 is involved in regulating ammonium transport. Among the 10 ammonium transporter genes examined here, expression of OsAMT1;1, OsAMT1;3, OsAMT2;1, and OsAMT4;1 was reduced in osdof18 mutants, demonstrating that the ammonium transporter genes function downstream of OsDOF18. Genes for nitrogen assimilation were also affected in the mutants. These results provide evidence that OsDOF18 mediates ammonium transport and nitrogen distribution, which then affects nitrogen use efficiency.
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Affiliation(s)
- Yunfei Wu
- Crop Biotech Institute and Graduate School of Biotechnology, Kyung Hee University, Yongin 17104,
Korea
| | - Wenzhu Yang
- Crop Biotech Institute and Graduate School of Biotechnology, Kyung Hee University, Yongin 17104,
Korea
| | - Jinhuan Wei
- Crop Biotech Institute and Graduate School of Biotechnology, Kyung Hee University, Yongin 17104,
Korea
| | - Hyeryung Yoon
- Crop Biotech Institute and Graduate School of Biotechnology, Kyung Hee University, Yongin 17104,
Korea
| | - Gynheung An
- Crop Biotech Institute and Graduate School of Biotechnology, Kyung Hee University, Yongin 17104,
Korea
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38
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Pii Y, Alessandrini M, Dall’Osto L, Guardini K, Prinsi B, Espen L, Zamboni A, Varanini Z. Time-Resolved Investigation of Molecular Components Involved in the Induction of [Formula: see text] High Affinity Transport System in Maize Roots. FRONTIERS IN PLANT SCIENCE 2016; 7:1657. [PMID: 27877183 PMCID: PMC5099785 DOI: 10.3389/fpls.2016.01657] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 10/20/2016] [Indexed: 05/18/2023]
Abstract
The induction, i.e., the rapid increase of nitrate ([Formula: see text]) uptake following the exposure of roots to the anion, was studied integrating physiological and molecular levels in maize roots. Responses to [Formula: see text] treatment were characterized in terms of changes in [Formula: see text] uptake rate and plasma membrane (PM) H+-ATPase activity and related to transcriptional and protein profiles of NRT2, NRT3, and PM H+-ATPase gene families. The behavior of transcripts and proteins of ZmNRT2s and ZmNRT3s suggested that the regulation of the activity of inducible high-affinity transport system (iHATS) is mainly based on the transcriptional/translational modulation of the accessory protein ZmNRT3.1A. Furthermore, ZmNRT2.1 and ZmNRT3.1A appear to be associated in a ∼150 kDa oligomer. The expression trend during the induction of the 11 identified PM H+-ATPase transcripts indicates that those mainly involved in the response to [Formula: see text] treatment are ZmHA2 and ZmHA4. Yet, partial correlation between the gene expression, protein levels and enzyme activity suggests an involvement of post-transcriptional and post-translational mechanisms of regulation. A non-denaturing Deriphat-PAGE approach allowed demonstrating for the first time that PM H+-ATPase can occur in vivo as hexameric complex together with the already described monomeric and dimeric forms.
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Affiliation(s)
- Youry Pii
- Faculty of Science and Technology, Free University of BolzanoBolzano, Italy
| | | | - Luca Dall’Osto
- Department of Biotechnology, University of VeronaVerona, Italy
| | - Katia Guardini
- Department of Biotechnology, University of VeronaVerona, Italy
| | - Bhakti Prinsi
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, University of MilanoMilano, Italy
| | - Luca Espen
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, University of MilanoMilano, Italy
| | - Anita Zamboni
- Department of Biotechnology, University of VeronaVerona, Italy
| | - Zeno Varanini
- Department of Biotechnology, University of VeronaVerona, Italy
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Massel K, Campbell BC, Mace ES, Tai S, Tao Y, Worland BG, Jordan DR, Botella JR, Godwin ID. Whole Genome Sequencing Reveals Potential New Targets for Improving Nitrogen Uptake and Utilization in Sorghum bicolor. FRONTIERS IN PLANT SCIENCE 2016; 7:1544. [PMID: 27826302 PMCID: PMC5078838 DOI: 10.3389/fpls.2016.01544] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 10/03/2016] [Indexed: 05/19/2023]
Abstract
Nitrogen (N) fertilizers are a major agricultural input where more than 100 million tons are supplied annually. Cereals are particularly inefficient at soil N uptake, where the unrecovered nitrogen causes serious environmental damage. Sorghum bicolor (sorghum) is an important cereal crop, particularly in resource-poor semi-arid regions, and is known to have a high NUE in comparison to other major cereals under limited N conditions. This study provides the first assessment of genetic diversity and signatures of selection across 230 fully sequenced genes putatively involved in the uptake and utilization of N from a diverse panel of sorghum lines. This comprehensive analysis reveals an overall reduction in diversity as a result of domestication and a total of 128 genes displaying signatures of purifying selection, thereby revealing possible gene targets to improve NUE in sorghum and cereals alike. A number of key genes appear to have been involved in selective sweeps, reducing their sequence diversity. The ammonium transporter (AMT) genes generally had low allelic diversity, whereas a substantial number of nitrate/peptide transporter 1 (NRT1/PTR) genes had higher nucleotide diversity in domesticated germplasm. Interestingly, members of the distinct race Guinea margaritiferum contained a number of unique alleles, and along with the wild sorghum species, represent a rich resource of new variation for plant improvement of NUE in sorghum.
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Affiliation(s)
- Karen Massel
- School of Agriculture and Food Sciences, The University of QueenslandBrisbane, QLD, Australia
| | - Bradley C. Campbell
- School of Agriculture and Food Sciences, The University of QueenslandBrisbane, QLD, Australia
| | - Emma S. Mace
- Department of Agriculture and FisheriesWarwick, QLD, Australia
| | | | - Yongfu Tao
- Queensland Alliance for Agriculture and Food Innovation, The University of QueenslandWarwick, QLD, Australia
| | - Belinda G. Worland
- School of Agriculture and Food Sciences, The University of QueenslandBrisbane, QLD, Australia
| | - David R. Jordan
- Queensland Alliance for Agriculture and Food Innovation, The University of QueenslandWarwick, QLD, Australia
| | - Jose R. Botella
- School of Agriculture and Food Sciences, The University of QueenslandBrisbane, QLD, Australia
| | - Ian D. Godwin
- School of Agriculture and Food Sciences, The University of QueenslandBrisbane, QLD, Australia
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Huang S, Chen S, Liang Z, Zhang C, Yan M, Chen J, Xu G, Fan X, Zhang Y. Knockdown of the partner protein OsNAR2.1 for high-affinity nitrate transport represses lateral root formation in a nitrate-dependent manner. Sci Rep 2015; 5:18192. [PMID: 26644084 PMCID: PMC4672285 DOI: 10.1038/srep18192] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 11/16/2015] [Indexed: 01/03/2023] Open
Abstract
The morphological plasticity of root systems is critical for plant survival, and understanding the mechanisms underlying root adaptation to nitrogen (N) fluctuation is critical for sustainable agriculture; however, the molecular mechanism of N-dependent root growth in rice remains unclear. This study aimed to identify the role of the complementary high-affinity NO3− transport protein OsNAR2.1 in NO3−-regulated rice root growth. Comparisons with wild-type (WT) plants showed that knockdown of OsNAR2.1 inhibited lateral root (LR) formation under low NO3− concentrations, but not under low NH4+ concentrations. 15N-labelling NO3− supplies (provided at concentrations of 0–10 mM) demonstrated that (i) defects in LR formation in mutants subjected to low external NO3− concentrations resulted from impaired NO3− uptake, and (ii) the mutants had significantly fewer LRs than the WT plants when root N contents were similar between genotypes. LR formation in osnar2.1 mutants was less sensitive to localised NO3− supply than LR formation in WT plants, suggesting that OsNAR2.1 may be involved in a NO3−-signalling pathway that controls LR formation. Knockdown of OsNAR2.1 inhibited LR formation by decreasing auxin transport from shoots to roots. Thus, OsNAR2.1 probably functions in both NO3− uptake and NO3−-signalling.
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Affiliation(s)
- Shuangjie Huang
- 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, P.R. China
| | - Si Chen
- 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, P.R. China
| | - Zhihao Liang
- 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, P.R. China
| | - Chenming Zhang
- 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, P.R. China
| | - Ming Yan
- 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, P.R. China
| | - Jingguang Chen
- 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, P.R. China
| | - 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, P.R. 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, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Yali Zhang
- 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, P.R. China
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Yu C, Liu Y, Zhang A, Su S, Yan A, Huang L, Ali I, Liu Y, Forde BG, Gan Y. MADS-box transcription factor OsMADS25 regulates root development through affection of nitrate accumulation in rice. PLoS One 2015; 10:e0135196. [PMID: 26258667 PMCID: PMC4530940 DOI: 10.1371/journal.pone.0135196] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 07/19/2015] [Indexed: 12/30/2022] Open
Abstract
MADS-box transcription factors are vital regulators participating in plant growth and development process and the functions of most of them are still unknown. ANR1 was reported to play a key role in controlling lateral root development through nitrate signal in Arabidopsis. OsMADS25 is one of five ANR1-like genes in Oryza Sativa and belongs to the ANR1 clade. Here we have investigated the role of OsMADS25 in the plant’s responses to external nitrate in Oryza Sativa. Our results showed that OsMADS25 protein was found in the nucleus as well as in the cytoplasm. Over-expression of OsMADS25 significantly promoted lateral and primary root growth as well as shoot growth in a nitrate-dependent manner in Arabidopsis. OsMADS25 overexpression in transgenic rice resulted in significantly increased primary root length, lateral root number, lateral root length and shoot fresh weight in the presence of nitrate. Down-regulation of OsMADS25 in transgenic rice exhibited significantly reduced shoot and root growth in the presence of nitrate. Furthermore, over-expression of OsMADS25 in transgenic rice promoted nitrate accumulation and significantly increased the expressions of nitrate transporter genes at high rates of nitrate supply while down-regulation of OsMADS25 produced the opposite effect. Taken together, our findings suggest that OsMADS25 is a positive regulator control lateral and primary root development in rice.
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Affiliation(s)
- Chunyan Yu
- Zhejiang Key Lab of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yihua Liu
- Zhejiang Key Lab of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Aidong Zhang
- Zhejiang Key Lab of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Sha Su
- Zhejiang Key Lab of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - An Yan
- Zhejiang Key Lab of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Linli Huang
- Zhejiang Key Lab of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Imran Ali
- Zhejiang Key Lab of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yu Liu
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Brian G. Forde
- Centre for Sustainable Agriculture, Lancaster Environment Centre, Lancaster University, Lancaster, United Kingdom
| | - Yinbo Gan
- Zhejiang Key Lab of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- * E-mail:
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Charrier A, Bérard JB, Bougaran G, Carrier G, Lukomska E, Schreiber N, Fournier F, Charrier AF, Rouxel C, Garnier M, Cadoret JP, Saint-Jean B. High-affinity nitrate/nitrite transporter genes (Nrt2) in Tisochrysis lutea: identification and expression analyses reveal some interesting specificities of Haptophyta microalgae. PHYSIOLOGIA PLANTARUM 2015; 154:572-90. [PMID: 25640753 DOI: 10.1111/ppl.12330] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 01/27/2015] [Accepted: 01/27/2015] [Indexed: 05/26/2023]
Abstract
Microalgae have a diversity of industrial applications such as feed, food ingredients, depuration processes and energy. However, microalgal production costs could be substantially improved by controlling nutrient intake. Accordingly, a better understanding of microalgal nitrogen metabolism is essential. Using in silico analysis from transcriptomic data concerning the microalgae Tisochrysis lutea, four genes encoding putative high-affinity nitrate/nitrite transporters (TlNrt2) were identified. Unlike most of the land plants and microalgae, cloning of genomic sequences and their alignment with complementary DNA (cDNA) sequences did not reveal the presence of introns in all TlNrt2 genes. The deduced TlNRT2 protein sequences showed similarities to NRT2 proteins of other phyla such as land plants and green algae. However, some interesting specificities only known among Haptophyta were also revealed, especially an additional sequence of 100 amino acids forming an atypical extracellular loop located between transmembrane domains 9 and 10 and the function of which remains to be elucidated. Analyses of individual TlNrt2 gene expression with different nitrogen sources and concentrations were performed. TlNrt2.1 and TlNrt2.3 were strongly induced by low NO3 (-) concentration and repressed by NH4 (+) substrate and were classified as inducible genes. TlNrt2.2 was characterized by a constitutive pattern whatever the substrate. Finally, TlNrt2.4 displayed an atypical response that was not reported earlier in literature. Interestingly, expression of TlNrt2.4 was rather related to internal nitrogen quota level than external nitrogen concentration. This first study on nitrogen metabolism of T. lutea opens avenues for future investigations on the function of these genes and their implication for industrial applications.
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Affiliation(s)
- Aurélie Charrier
- Physiology and Biotechnology of Algae Laboratory, IFREMER, Nantes, 44311, France
| | - Jean-Baptiste Bérard
- Physiology and Biotechnology of Algae Laboratory, IFREMER, Nantes, 44311, France
| | - Gaël Bougaran
- Physiology and Biotechnology of Algae Laboratory, IFREMER, Nantes, 44311, France
| | - Grégory Carrier
- Physiology and Biotechnology of Algae Laboratory, IFREMER, Nantes, 44311, France
| | - Ewa Lukomska
- Physiology and Biotechnology of Algae Laboratory, IFREMER, Nantes, 44311, France
| | - Nathalie Schreiber
- Physiology and Biotechnology of Algae Laboratory, IFREMER, Nantes, 44311, France
| | - Flora Fournier
- Physiology and Biotechnology of Algae Laboratory, IFREMER, Nantes, 44311, France
| | - Aurélie F Charrier
- Physiology and Biotechnology of Algae Laboratory, IFREMER, Nantes, 44311, France
| | - Catherine Rouxel
- Physiology and Biotechnology of Algae Laboratory, IFREMER, Nantes, 44311, France
| | - Matthieu Garnier
- Physiology and Biotechnology of Algae Laboratory, IFREMER, Nantes, 44311, France
| | - Jean-Paul Cadoret
- Physiology and Biotechnology of Algae Laboratory, IFREMER, Nantes, 44311, France
| | - Bruno Saint-Jean
- Physiology and Biotechnology of Algae Laboratory, IFREMER, Nantes, 44311, France
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Pellizzaro A, Clochard T, Planchet E, Limami AM, Morère-Le Paven MC. Identification and molecular characterization of Medicago truncatula NRT2 and NAR2 families. PHYSIOLOGIA PLANTARUM 2015; 154:256-69. [PMID: 25430977 DOI: 10.1111/ppl.12314] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2014] [Revised: 11/22/2014] [Accepted: 11/24/2014] [Indexed: 05/24/2023]
Abstract
Nitrate transporters received little attention to legumes probably because these species are able to adapt to N starvation by developing biological N2 fixation. Still it is important to study nitrate transport systems in legumes because nitrate intervenes as a signal in regulation of nodulation probably through nitrate transporters. The aim of this work is to achieve a molecular characterization of nitrate transporter 2 (NRT2) and NAR2 (NRT3) families to allow further work that would unravel their involvement in nitrate transport and signaling. Browsing the latest version of the Medicago truncatula genome annotation (v4 version) revealed three putative NRT2 members that we have named MtNRT2.1 (Medtr4g057890.1), MtNRT2.2 (Medtr4g057865.1) and MtNRT2.3 (Medtr8g069775.1) and two putative NAR2 members we named MtNAR2.1 (Medtr4g104730.1) and MtNAR2.2 (Medtr4g104700.1). The regulation and the spatial expression profiles of MtNRT2.1, the coincidence of its expression with that of MtNAR2.1 and MtNAR2.2 and the size of the encoded protein with 12 transmembrane (TM) spanning regions strongly support the idea that MtNRT2.1 is a nitrate transporter with a major contribution to the high-affinity transport system (HATS), while a very low level of expression characterized MtNRT2.2. Unlike MtNRT2.1, MtNRT2.3 showed a lower level of expression in the root system but was expressed in the shoots and in the nodules thus suggesting an involvement of the encoded protein in nitrate transport inside the plant and/or in nitrate signaling pathways controlling post-inoculation processes that govern nodule functioning.
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Affiliation(s)
- Anthoni Pellizzaro
- Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR4207 QUASAV, 2 Boulevard Lavoisier, F-49045 Angers, France
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, 42 rue Georges Morel, F-49071 Beaucouzé, France
| | - Thibault Clochard
- Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR4207 QUASAV, 2 Boulevard Lavoisier, F-49045 Angers, France
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, 42 rue Georges Morel, F-49071 Beaucouzé, France
| | - Elisabeth Planchet
- Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR4207 QUASAV, 2 Boulevard Lavoisier, F-49045 Angers, France
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, 42 rue Georges Morel, F-49071 Beaucouzé, France
| | - Anis M Limami
- Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR4207 QUASAV, 2 Boulevard Lavoisier, F-49045 Angers, France
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, 42 rue Georges Morel, F-49071 Beaucouzé, France
| | - Marie-Christine Morère-Le Paven
- Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR4207 QUASAV, 2 Boulevard Lavoisier, F-49045 Angers, France
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, 42 rue Georges Morel, F-49071 Beaucouzé, France
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Li Y, Ouyang J, Wang YY, Hu R, Xia K, Duan J, Wang Y, Tsay YF, Zhang M. Disruption of the rice nitrate transporter OsNPF2.2 hinders root-to-shoot nitrate transport and vascular development. Sci Rep 2015; 5:9635. [PMID: 25923512 PMCID: PMC5386202 DOI: 10.1038/srep09635] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 03/09/2015] [Indexed: 11/08/2022] Open
Abstract
Plants have evolved to express some members of the nitrate transporter 1/peptide transporter family (NPF) to uptake and transport nitrate. However, little is known of the physiological and functional roles of this family in rice (Oryza sativa L.). Here, we characterized the vascular specific transporter OsNPF2.2. Functional analysis using cDNA-injected Xenopus laevis oocytes revealed that OsNPF2.2 is a low-affinity, pH-dependent nitrate transporter. Use of a green fluorescent protein tagged OsNPF2.2 showed that the transporter is located in the plasma membrane in the rice protoplast. Expression analysis showed that OsNPF2.2 is nitrate inducible and is mainly expressed in parenchyma cells around the xylem. Disruption of OsNPF2.2 increased nitrate concentration in the shoot xylem exudate when nitrate was supplied after a deprivation period; this result suggests that OsNPF2.2 may participate in unloading nitrate from the xylem. Under steady-state nitrate supply, the osnpf2.2 mutants maintained high levels of nitrate in the roots and low shoot:root nitrate ratios; this observation suggests that OsNPF2.2 is involved in root-to-shoot nitrate transport. Mutation of OsNPF2.2 also caused abnormal vasculature and retarded plant growth and development. Our findings demonstrate that OsNPF2.2 can unload nitrate from the xylem to affect the root-to-shoot nitrate transport and plant development.
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Affiliation(s)
- Yuge Li
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Jie Ouyang
- Rice Institute, Chongqing Academy of Agricultural Sciences, Chongqing 401329, China
| | - Ya-Yun Wang
- Department of Life Science, National Taiwan University, Taipei, Taiwan
| | - Rui Hu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kuaifei Xia
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Jun Duan
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Yaqin Wang
- Guangdong Key Lab of Biotechnology for Plant Development, College of Life Science, South China Normal University, Guangzhou 510631, China
| | - Yi-Fang Tsay
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Mingyong Zhang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
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LeNRT2.3 functions in nitrate acquisition and long-distance transport in tomato. FEBS Lett 2015; 589:1072-9. [DOI: 10.1016/j.febslet.2015.03.016] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 02/27/2015] [Accepted: 03/13/2015] [Indexed: 01/03/2023]
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Reddy MM, Ulaganathan K. Nitrogen Nutrition, Its Regulation and Biotechnological Approaches to Improve Crop Productivity. ACTA ACUST UNITED AC 2015. [DOI: 10.4236/ajps.2015.618275] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Araki R, Kousaka K, Namba K, Murata Y, Murata J. 2'-Deoxymugineic acid promotes growth of rice (Oryza sativa L.) by orchestrating iron and nitrate uptake processes under high pH conditions. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 81:233-46. [PMID: 25393516 PMCID: PMC4309410 DOI: 10.1111/tpj.12722] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 10/24/2014] [Accepted: 11/03/2014] [Indexed: 05/20/2023]
Abstract
Poaceae plants release 2'-deoxymugineic acid (DMA) and related phytosiderophores to chelate iron (Fe), which often exists as insoluble Fe(III) in the rhizosphere, especially under high pH conditions. Although the molecular mechanisms behind the biosynthesis and secretion of DMA have been studied extensively, little information is known about whether DMA has biological roles other than chelating Fe in vivo. Here, we demonstrate that hydroponic cultures of rice (Oryza sativa) seedlings show almost complete restoration in shoot height and soil-plant analysis development (SPAD) values after treatment with 3-30 μm DMA at high pH (pH 8.0), compared with untreated control seedlings at normal pH (pH 5.8). These changes were accompanied by selective accumulation of Fe over other metals. While this enhanced growth was evident under high pH conditions, DMA application also enhanced seedling growth under normal pH conditions in which Fe was fairly accessible. Microarray and qRT-PCR analyses revealed that exogenous DMA application attenuated the increased expression levels of various genes related to Fe transport and accumulation. Surprisingly, despite the preferential utilization of ammonium over nitrate as a nitrogen source by rice, DMA application also increased nitrate reductase activity and the expression of genes encoding high-affinity nitrate transporters and nitrate reductases, all of which were otherwise considerably lower under high pH conditions. These data suggest that exogenous DMA not only plays an important role in facilitating the uptake of environmental Fe, but also orchestrates Fe and nitrate assimilation for optimal growth under high pH conditions.
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Affiliation(s)
- Ryoichi Araki
- Division of Integrative Biomolecular Function, Bioorganic Research Institute, Suntory Foundation for Life Sciences1-1-1 Wakayamadai, Shimamoto, Mishima, Osaka, 618-8503, Japan
| | - Kayoko Kousaka
- Division of Integrative Biomolecular Function, Bioorganic Research Institute, Suntory Foundation for Life Sciences1-1-1 Wakayamadai, Shimamoto, Mishima, Osaka, 618-8503, Japan
| | - Kosuke Namba
- Department of Chemistry, Graduate School of Science, Hokkaido UniversityKita-ku, Sapporo, 060-0810, Japan
| | - Yoshiko Murata
- Division of Integrative Biomolecular Function, Bioorganic Research Institute, Suntory Foundation for Life Sciences1-1-1 Wakayamadai, Shimamoto, Mishima, Osaka, 618-8503, Japan
| | - Jun Murata
- Division of Integrative Biomolecular Function, Bioorganic Research Institute, Suntory Foundation for Life Sciences1-1-1 Wakayamadai, Shimamoto, Mishima, Osaka, 618-8503, Japan
- *For correspondence (e-mail )
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Kobayashi S, Satone H, Tan E, Kurokochi H, Asakawa S, Liu S, Takano T. Transcriptional responses of a bicarbonate-tolerant monocot, Puccinellia tenuiflora, and a related bicarbonate-sensitive species, Poa annua, to NaHCO3 stress. Int J Mol Sci 2014; 16:496-509. [PMID: 25551599 PMCID: PMC4307258 DOI: 10.3390/ijms16010496] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 12/23/2014] [Indexed: 11/16/2022] Open
Abstract
Puccinellia tenuiflora is an alkaline salt-tolerant monocot found in saline-alkali soil in China. To identify the genes which are determining the higher tolerance of P. tenuiflora compared to bicarbonate sensitive species, we examined the responses of P. tenuiflora and a related bicarbonate-sensitive Poeae plant, Poa annua, to two days of 20 mM NaHCO3 stress by RNA-seq analysis. We obtained 28 and 38 million reads for P. tenuiflora and P. annua, respectively. For each species, the reads of both unstressed and stressed samples were combined for de novo assembly of contigs. We obtained 77,329 contigs for P. tenuiflora and 115,335 contigs for P.annua. NaHCO3 stress resulted in greater than two-fold absolute expression value changes in 157 of the P. tenuiflora contigs and 1090 of P. annua contigs. Homologs of the genes involved in Fe acquisition, which are important for the survival of plants under alkaline stress, were up-regulated in P. tenuiflora and down-regulated in P. annua. The smaller number of the genes differentially regulated in P. tenuiflora suggests that the genes regulating bicarbonate tolerance are constitutively expressed in P. tenuiflora.
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Affiliation(s)
- Shio Kobayashi
- Asian Natural Environmental Science Center (ANESC), the University of Tokyo, Nishitokyo-shi, Tokyo 188-0002, Japan.
| | - Hina Satone
- Graduate School of Agricultural and Life Sciences, the University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan.
| | - Engkong Tan
- Graduate School of Agricultural and Life Sciences, the University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan.
| | - Hiroyuki Kurokochi
- Asian Natural Environmental Science Center (ANESC), the University of Tokyo, Nishitokyo-shi, Tokyo 188-0002, Japan.
| | - Shuichi Asakawa
- Graduate School of Agricultural and Life Sciences, the University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan.
| | - Shenkui Liu
- Alkali Soil Natural Environmental Science Center (ASNESC), Northeast Forestry University, Harbin Hexing Road, Harbin 150040, China.
| | - Tetsuo Takano
- Asian Natural Environmental Science Center (ANESC), the University of Tokyo, Nishitokyo-shi, Tokyo 188-0002, Japan.
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Liu X, Huang D, Tao J, Miller AJ, Fan X, Xu G. Identification and functional assay of the interaction motifs in the partner protein OsNAR2.1 of the two-component system for high-affinity nitrate transport. THE NEW PHYTOLOGIST 2014; 204:74-80. [PMID: 25103875 PMCID: PMC4232926 DOI: 10.1111/nph.12986] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 07/15/2014] [Indexed: 05/21/2023]
Abstract
A partner protein, NAR2, is essential for high-affinity nitrate transport of the NRT2 protein in plants. However, the NAR2 motifs that interact with NRT2s for their plasma membrane (PM) localization and nitrate transporter activity have not been functionally characterized. In this study, OsNAR2.1 mutations with different carbon (C)-terminal deletions and nine different point mutations in the conserved regions of NAR2 homologs in plants were generated to explore the essential motifs involved in the interaction with OsNRT2.3a. Screening using the membrane yeast two-hybrid system and Xenopus oocytes for nitrogen-15 ((15)N) uptake demonstrated that either R100G or D109N point mutations impaired the OsNAR2.1 interaction with OsNRT2.3a. Western blotting and visualization using green fluorescent protein fused to either the N- or C-terminus of OsNAR2.1 indicated that OsNAR2.1 is expressed in both the PM and cytoplasm. The split-yellow fluorescent protein (YFP)/BiFC analyses indicated that OsNRT2.3a was targeted to the PM in the presence of OsNAR2.1, while either R100G or D109N mutation resulted in the loss of OsNRT2.3a-YFP signal in the PM. Based on these results, arginine 100 and aspartic acid 109 of the OsNAR2.1 protein are key amino acids in the interaction with OsNRT2.3a, and their interaction occurs in the PM but not cytoplasm.
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Affiliation(s)
- Xiaoqin Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural UniversityNanjing, 210095, China
- MOA Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Nanjing Agricultural UniversityNanjing, 210095, China
| | - Daimin Huang
- MOA Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Nanjing Agricultural UniversityNanjing, 210095, China
| | - Jinyuan Tao
- MOA Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Nanjing Agricultural UniversityNanjing, 210095, China
| | - Anthony J Miller
- Metabolic Biology Department, John Innes CentreNorwich Research Park, Norwich, NR4 7UH, UK
| | - Xiaorong Fan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural UniversityNanjing, 210095, China
- MOA Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Nanjing Agricultural UniversityNanjing, 210095, China
| | - Guohua Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural UniversityNanjing, 210095, China
- MOA Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Nanjing Agricultural UniversityNanjing, 210095, China
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50
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Paz RC, Rocco RA, Jiménez-Bremont JF, Rodríguez-Kessler M, Becerra-Flora A, Menéndez AB, Ruíz OA. Identification of differentially expressed genes potentially involved in the tolerance of Lotus tenuis to long-term alkaline stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2014; 82:279-288. [PMID: 25025825 DOI: 10.1016/j.plaphy.2014.06.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 06/17/2014] [Indexed: 06/03/2023]
Abstract
Soil alkalinity is one of the most serious agricultural problems limiting crop yields. The legume Lotus tenuis is an important forage acknowledged by its ability to naturally grow in alkaline soils. To gain insight into the molecular responses that are activated by alkalinity in L. tenuis plants, subtractive cDNA libraries were generated from leaves and roots of these plants. Total RNAs of non-stressed plants (pH 5.8; E.C. 1.2), and plants stressed by the addition of 10 mM of NaHCO3 (pH 9.0; E.C. 1.9), were used as source of the driver and the tester samples, respectively. RNA samples were collected after 14 and 28 days of treatment. A total of 158 unigenes from leaves and 92 unigenes from roots were obtained and classified into 11 functional categories. Unigenes from these categories (4 for leaves and 8 for roots), that were related with nutrient metabolism and oxidative stress relief were selected, and their differential expression analyzed by qRT-PCR. These genes were found to be differentially expressed in a time dependent manner in L. tenuis during the alkaline stress application. Data generated from this study will contribute to the understanding of the general molecular mechanisms associated to plant tolerance under long-term alkaline stress in plants.
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Affiliation(s)
- Rosalía Cristina Paz
- Grupo INTERBIODES (Interacciones Biológicas del Desierto/Biological Interactions of Desert), CIGEOBIO (FCEFyN, UNSJ/CONICET), Dpto. de Biología, Av. Ignacio de la Roza 590 (Oeste), J5402DCS Rivadavia, San Juan, Argentina.
| | - Rubén Anibal Rocco
- Unidad de Biotecnología 1, IIB-IINTECH/UNSAM-CONICET, Chascomús, Buenos Aires, Argentina.
| | - Juan Francisco Jiménez-Bremont
- Instituto Potosino de Investigación Científica y Tecnológica (IPICyT), Camino a la Presa de San José No. 2055, Lomas 4a Sección, CP 78216 San Luis Potosí, SLP, México.
| | - Margarita Rodríguez-Kessler
- Facultad de Ciencias, Universidad Autónoma de San Luis Potosí, Av. Salvador Nava s/n, Zona Universitaria, C.P. 78290 San Luis Potosí, SLP, México.
| | - Alicia Becerra-Flora
- Instituto Potosino de Investigación Científica y Tecnológica (IPICyT), Camino a la Presa de San José No. 2055, Lomas 4a Sección, CP 78216 San Luis Potosí, SLP, México.
| | - Ana Bernardina Menéndez
- Departamento de Biodiversidad y Biología Experimental, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Argentina; PROPLAME-PRHIDEB (CONICET), Argentina.
| | - Oscar Adolfo Ruíz
- Unidad de Biotecnología 1, IIB-IINTECH/UNSAM-CONICET, Chascomús, Buenos Aires, Argentina.
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