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Salama EAA, Kambale R, Gnanapanditha Mohan SV, Premnath A, Fathy Yousef A, Moursy ARA, Abdelsalam NR, Abd El Moneim D, Muthurajan R, Manikanda Boopathi N. Empowering rice breeding with NextGen genomics tools for rapid enhancement nitrogen use efficiency. Gene 2024; 927:148715. [PMID: 38909967 DOI: 10.1016/j.gene.2024.148715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 06/17/2024] [Accepted: 06/19/2024] [Indexed: 06/25/2024]
Abstract
As rice has no physiological capacity of fixing nitrogen in the soil, its production had always been reliant on the external application of nitrogen (N) to ensure enhanced productivity. In the light of improving nitrogen use efficiency (NUE) in rice, several advanced agronomic strategies have been proposed. However, the soared increase of the prices of N fertilizers and subsequent environmental downfalls caused by the excessive use of N fertilizers, reinforces the prerequisite adaptation of other sustainable, affordable, and globally acceptable strategies. An appropriate alternative approach would be to develop rice cultivars with better NUE. Conventional breeding techniques, however, have had only sporadic success in improving NUE, and hence, this paper proposes a new schema that employs the wholesome benefits of the recent advancements in omics technologies. The suggested approach promotes multidisciplinary research, since such cooperation enables the synthesis of many viewpoints, approaches, and data that result in a comprehensive understanding of NUE in rice. Such collaboration also encourages innovation that leads to developing rice varieties that use nitrogen more effectively, facilitate smart technology transfer, and promotes the adoption of NUE practices by farmers and stakeholders to minimize ecological impact and contribute to a sustainable agricultural future.
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Affiliation(s)
- Ehab A A Salama
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641003, India; Agricultural Botany Department (Genetics), Faculty of Agriculture Saba Basha, Alexandria University, Alexandria 21531, Egypt.
| | - Rohit Kambale
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641003, India.
| | - Shobhana V Gnanapanditha Mohan
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641003, India.
| | - Ameena Premnath
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641003, India.
| | - Ahmed Fathy Yousef
- Department of Horticulture, College of Agriculture, University of Al-Azhar (Branch Assiut), Assiut 71524, Egypt.
| | - Ali R A Moursy
- Soil and Water Department, Faculty of Agriculture, Sohag University, Sohag 82524, Egypt.
| | - Nader R Abdelsalam
- Agricultural Botany Department (Genetics), Faculty of Agriculture Saba Basha, Alexandria University, Alexandria 21531, Egypt.
| | - Diaa Abd El Moneim
- Department of Plant Production (Genetic Branch), Faculty of Environmental Agricultural Sciences, Arish University, El-Arish 45511, Egypt.
| | - Raveendran Muthurajan
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641003, India.
| | - Narayanan Manikanda Boopathi
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641003, India.
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Wang Y, Liu H, Bai L, Liu R, Jiang H, Tan J, Chen J. Overexpression of OsNAR2.1 by OsNAR2.1 promoter increases drought resistance by increasing the expression of OsPLDα1 in rice. BMC PLANT BIOLOGY 2024; 24:321. [PMID: 38654179 PMCID: PMC11040742 DOI: 10.1186/s12870-024-05012-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 04/11/2024] [Indexed: 04/25/2024]
Abstract
BACKGROUND pOsNAR2.1:OsNAR2.1 expression could significantly increase nitrogen uptake efficiency and grain yield of rice. RESULT This study reported the effects of overexpression of OsNAR2.1 by OsNAR2.1 promoter on physiological and agronomic traits associated with drought tolerance. In comparison to the wild-type (WT), the pOsNAR2.1:OsNAR2.1 transgenic lines exhibited a significant improvement in survival rate when subjected to drought stress and then irrigation. Under limited water supply conditions, compared with WT, the photosynthesis and water use efficiency (WUE) of transgenic lines were increased by 39.2% and 28.8%, respectively. Finally, the transgenic lines had 25.5% and 66.4% higher grain yield than the WT under full watering and limited water supply conditions, respectively. Compared with the WT, the agronomic nitrogen use efficiency (NUE) of transgenic lines increased by 25.5% and 66.4% under full watering and limited water supply conditions, and the N recovery efficiency of transgenic lines increased by 29.3% and 50.2%, respectively. The interaction between OsNAR2.1 protein and OsPLDα1 protein was verified by yeast hybrids. After drought treatment, PLDα activity on the plasma membrane of the transgenic line increased 85.0% compared with WT. CONCLUSION These results indicated that pOsNAR2.1:OsNAR2.1 expression could improve the drought resistance of rice by increasing nitrogen uptake and regulating the expression of OsPLDα1.
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Affiliation(s)
- Yamei Wang
- School of Agriculture, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, 518107, China
| | - Hongyan Liu
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, Hainan, 572025, China
| | - Lu Bai
- School of Agriculture, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, 518107, China
| | - Ruifang Liu
- The High School Affiliated to Renmin, University of China, Shenzhen, Guangdong, 518119, China
| | - Hongzhen Jiang
- School of Agriculture, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, 518107, China
| | - Jinfang Tan
- School of Agriculture, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, 518107, China
| | - Jingguang Chen
- School of Agriculture, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, 518107, China.
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Xu N, Cheng L, Kong Y, Chen G, Zhao L, Liu F. Functional analyses of the NRT2 family of nitrate transporters in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2024; 15:1351998. [PMID: 38501135 PMCID: PMC10944928 DOI: 10.3389/fpls.2024.1351998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 02/06/2024] [Indexed: 03/20/2024]
Abstract
Nitrogen is an essential macronutrient for plant growth and development. Nitrate is the major form of nitrogen acquired by most crops and also serves as a vital signaling molecule. Nitrate is absorbed from the soil into root cells usually by the low-affinity NRT1 NO3 - transporters and high-affinity NRT2 NO3 - transporters, with NRT2s serving to absorb NO3 - under NO3 -limiting conditions. Seven NRT2 members have been identified in Arabidopsis, and they have been shown to be involved in various biological processes. In this review, we summarize the spatiotemporal expression patterns, localization, and biotic and abiotic responses of these transporters with a focus on recent advances in the current understanding of the functions of the seven AtNRT2 genes. This review offers beneficial insight into the mechanisms by which plants adapt to changing environmental conditions and provides a theoretical basis for crop research in the near future.
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Affiliation(s)
- Na Xu
- School of Biological Science, Jining Medical University, Rizhao, Shandong, China
| | - Li Cheng
- School of Biological Science, Jining Medical University, Rizhao, Shandong, China
| | - Yuan Kong
- School of Biological Science, Jining Medical University, Rizhao, Shandong, China
| | - Guiling Chen
- School of Biological Science, Jining Medical University, Rizhao, Shandong, China
| | - Lufei Zhao
- Agricultural Science and Engineering School, Liaocheng University, Liaocheng, Shandong, China
| | - Fei Liu
- School of Biological Science, Jining Medical University, Rizhao, Shandong, China
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Zhang Z, Diao R, Sun J, Liu Y, Zhao M, Wang Q, Xu Z, Zhong B. Diversified molecular adaptations of inorganic nitrogen assimilation and signaling machineries in plants. THE NEW PHYTOLOGIST 2024; 241:2108-2123. [PMID: 38155438 DOI: 10.1111/nph.19508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 12/11/2023] [Indexed: 12/30/2023]
Abstract
Plants evolved sophisticated machineries to monitor levels of external nitrogen supply, respond to nitrogen demand from different tissues and integrate this information for coordinating its assimilation. Although roles of inorganic nitrogen in orchestrating developments have been studied in model plants and crops, systematic understanding of the origin and evolution of its assimilation and signaling machineries remains largely unknown. We expanded taxon samplings of algae and early-diverging land plants, covering all main lineages of Archaeplastida, and reconstructed the evolutionary history of core components involved in inorganic nitrogen assimilation and signaling. Most components associated with inorganic nitrogen assimilation were derived from the ancestral Archaeplastida. Improvements of assimilation machineries by gene duplications and horizontal gene transfers were evident during plant terrestrialization. Clusterization of genes encoding nitrate assimilation proteins might be an adaptive strategy for algae to cope with changeable nitrate availability in different habitats. Green plants evolved complex nitrate signaling machinery that was stepwise improved by domains shuffling and regulation co-option. Our study highlights innovations in inorganic nitrogen assimilation and signaling machineries, ranging from molecular modifications of proteins to genomic rearrangements, which shaped developmental and metabolic adaptations of plants to changeable nutrient availability in environments.
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Affiliation(s)
- Zhenhua Zhang
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Runjie Diao
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Jingyan Sun
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Yannan Liu
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Mengru Zhao
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Qiuping Wang
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Zilong Xu
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Bojian Zhong
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, 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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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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Wu J, Yang S, Chen N, Jiang Q, Huang L, Qi J, Xu G, Shen L, Yu H, Fan X, Gan Y. Nuclear translocation of OsMADS25 facilitated by OsNAR2.1 in reponse to nitrate signals promotes rice root growth by targeting OsMADS27 and OsARF7. PLANT COMMUNICATIONS 2023; 4:100642. [PMID: 37353931 PMCID: PMC10721473 DOI: 10.1016/j.xplc.2023.100642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 05/24/2023] [Accepted: 06/20/2023] [Indexed: 06/25/2023]
Abstract
Nitrate is an important nitrogen source and signaling molecule that regulates plant growth and development. Although several components of the nitrate signaling pathway have been identified, the detailed mechanisms are still unclear. Our previous results showed that OsMADS25 can regulate root development in response to nitrate signals, but the mechanism is still unknown. Here, we try to answer two key questions: how does OsMADS25 move from the cytoplasm to the nucleus, and what are the direct target genes activated by OsMADS25 to regulate root growth after it moves to the nucleus in response to nitrate? Our results demonstrated that OsMADS25 moves from the cytoplasm to the nucleus in the presence of nitrate in an OsNAR2.1-dependent manner. Chromatin immunoprecipitation sequencing, chromatin immunoprecipitation qPCR, yeast one-hybrid, and luciferase experiments showed that OsMADS25 directly activates the expression of OsMADS27 and OsARF7, which are reported to be associated with root growth. Finally, OsMADS25-RNAi lines, the Osnar2.1 mutant, and OsMADS25-RNAi Osnar2.1 lines exhibited significantly reduced root growth compared with the wild type in response to nitrate supply, and expression of OsMADS27 and OsARF7 was significantly suppressed in these lines. Collectively, these results reveal a new mechanism by which OsMADS25 interacts with OsNAR2.1. This interaction is required for nuclear accumulation of OsMADS25, which promotes OsMADS27 and OsARF7 expression and root growth in a nitrate-dependent manner.
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Affiliation(s)
- Junyu Wu
- Zhejiang Key Laboratory of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310000, China
| | - Shuaiqi Yang
- Zhejiang Key Laboratory of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310000, China
| | - Nana Chen
- Zhejiang Key Laboratory of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310000, China
| | - Qining Jiang
- Zhejiang Key Laboratory of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310000, China
| | - Linli Huang
- Zhejiang Key Laboratory of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310000, China
| | - Jiaxuan Qi
- Zhejiang Key Laboratory of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310000, China
| | - Guohua Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Lisha Shen
- Temasek Life Sciences Laboratory and Department of Biological Sciences, National University of Singapore, 1 Research Link, Singapore 117604, Singapore
| | - Hao Yu
- Temasek Life Sciences Laboratory and Department of Biological Sciences, National University of Singapore, 1 Research Link, Singapore 117604, Singapore
| | - Xiaorong Fan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China.
| | - Yinbo Gan
- Zhejiang Key Laboratory of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310000, China.
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Hajibarat Z, Saidi A, Ghazvini H, Hajibarat Z. Comparative analysis of physiological traits and gene expression patterns in nitrogen deficiency among barley cultivars. J Genet Eng Biotechnol 2023; 21:110. [PMID: 37947941 PMCID: PMC10638351 DOI: 10.1186/s43141-023-00567-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 10/26/2023] [Indexed: 11/12/2023]
Abstract
BACKGROUND Nitrogen is one of the most important mineral nutrients for plants and is absorbed by the root system mainly in the inorganic form (NH+4 and NO-3). Plants absorb nitrogen as a food source for growth, biomass production, and development. Nitrogen is mainly absorbed as nitrate, which is the most common source of nitrogen available to higher plants. One of the unique features of nitrate transport is that NO-3 is both a substrate for transport and an inducer of NO-3 transport systems in genes and at physiological levels. METHODS In the present study, morphological and physiological traits (chlorophyll a/b, total chlorophyll, and carotenoid, antioxidant enzymes, and protein content), correlation between traits and gene expression, and principle component analysis of traits among five barley cultivars were measured in response to nitrogen deficiency (ND). The starved plants were transferred to a nutrient solution containing 0.2 mM and 2 mM NO-3 up to 7 and 14 days after ND application and non-stressed conditions, respectively. RESULTS Gene expression analysis revealed that the 10 HvNRT2 genes were induced in the leaf and root tissues at 7 and 14 days after ND treatments in five barley cultivars. Expression of NRT2 genes by relative quantitative qRT-PCR analysis for 10 HvNRT2 genes were determined. Based on the gene expression, HvNRT2.1, HvNRT2.2, and HvNRT2.4 were strongly induced by NO-3, peaking at 7 and 14 days after ND treatment. In contrast, the HvNRT2.4 showed only moderate induction in both leaves and roots. From our results, the Reyhan cultivar showed a significant increase in root fresh weight (RFW), protein content, and antioxidant enzyme activity in roots at 7 and 14 days after ND treatment as compared to the non-stressed condition. A highly positive correlation was observed between root catalase (CATr) and HvNRT2.2/2.5/2.6 leaves. CONCLUSION The expression of HvNRT2.4 is increased during long-term nitrogen starvation, while the expression of HvNRT2.1 and HvNRT2.2 are transiently increased by ND. Based on physiological and morphological traits and molecular mechanisms, the Reyhan is considered a tolerant cultivar under ND condition.
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Affiliation(s)
- Zohreh Hajibarat
- Department of Plant Sciences and Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Abbas Saidi
- Department of Plant Sciences and Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran.
| | - Habibollah Ghazvini
- Department of Cearal Research, Seed and Plant Improvement Institute (SPII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Zahra Hajibarat
- Department of Plant Sciences and Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
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Ma X, Nian J, Yu H, Zhang F, Feng T, Kou L, Zhang J, Wang D, Li H, Chen L, Dong G, Xie X, Wang G, Qian Q, Li J, Zuo J. Linking glucose signaling to nitrogen utilization by the OsHXK7-ARE4 complex in rice. Dev Cell 2023; 58:1489-1501.e5. [PMID: 37413992 DOI: 10.1016/j.devcel.2023.06.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 04/09/2023] [Accepted: 06/09/2023] [Indexed: 07/08/2023]
Abstract
How reciprocal regulation of carbon and nitrogen metabolism works is a long-standing question. In plants, glucose and nitrate are proposed to act as signaling molecules, regulating carbon and nitrogen metabolism via largely unknown mechanisms. Here, we show that the MYB-related transcription factor ARE4 coordinates glucose signaling and nitrogen utilization in rice. ARE4 is retained in the cytosol in complexing with the glucose sensor OsHXK7. Upon sensing a glucose signal, ARE4 is released, is translocated into the nucleus, and activates the expression of a subset of high-affinity nitrate transporter genes, thereby boosting nitrate uptake and accumulation. This regulatory scheme displays a diurnal pattern in response to circadian changes of soluble sugars. The are4 mutations compromise in nitrate utilization and plant growth, whereas overexpression of ARE4 increases grain size. We propose that the OsHXK7-ARE4 complex links glucose to the transcriptional regulation of nitrogen utilization, thereby coordinating carbon and nitrogen metabolism.
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Affiliation(s)
- Xiaohui Ma
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinqiang Nian
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hong Yu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Fengxia Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Tianpeng Feng
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liquan Kou
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jian Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Danfeng Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hanwen Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lichao Chen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guojun Dong
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Xianzhi Xie
- Institute of Wetland Agriculture and Ecology, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Guodong Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qian Qian
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Jiayang Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Jianru Zuo
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; C.A.S. Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Beijing 100101, China; Hainan Seed Laboratory, Sanya 572025, Hainan, China.
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10
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Phan NTH, Draye X, Pham CV, Bertin P. Identification of quantitative trait loci controlling nitrogen use efficiency-related traits in rice at the seedling stage under salt condition by genome-wide association study. FRONTIERS IN PLANT SCIENCE 2023; 14:1197271. [PMID: 37575915 PMCID: PMC10415682 DOI: 10.3389/fpls.2023.1197271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 07/04/2023] [Indexed: 08/15/2023]
Abstract
Rice cultivation is facing both salt intrusion and overuse of nitrogen fertilizers. Hence, breeding new varieties aiming to improve nitrogen use efficiency (NUE), especially under salt conditions, is indispensable. We selected 2,391 rice accessions from the 3K Rice Genomes Project to evaluate the dry weight under two N concentrations [2.86 mM - standard N (SN), and 0.36 mM - low N (LN)] crossed with two NaCl concentrations [0 (0Na) and 60 mM (60Na)] at the seedling stage. Genome-wide association studies for shoot, root, and plant dry weight (DW) were carried out. A total of 55 QTLs - 32, 16, and 7 in the whole, indica, and japonica panel - associated with one of the tested traits were identified. Among these, 27 QTLs co-localized with previously identified QTLs for DW-related traits while the other 28 were newly detected; 24, 8, 11, and 4 QTLs were detected in SN-0Na, LN-0Na, SN-60Na, and LN-60Na, respectively, and the remaining 8 QTLs were for the relative plant DW between treatments. Three of the 11 QTLs in SN-60Na were close to the regions containing three QTLs detected in SN-0Na. Eleven candidate genes for eight important QTLs were identified. Only one of them was detected in both SN-0Na and SN-60Na, while 5, 0, 3, and 2 candidate genes were identified only once under SN-0Na, LN-0Na, SN-60Na, and LN-60Na, respectively. The identified QTLs and genes provide useful materials and genetic information for future functional characterization and genetic improvement of NUE in rice, especially under salt conditions.
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Affiliation(s)
- Nhung Thi Hong Phan
- Earth and Life Institute, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
- Agronomy Faculty, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - Xavier Draye
- Earth and Life Institute, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Cuong Van Pham
- Agronomy Faculty, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - Pierre Bertin
- Earth and Life Institute, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
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11
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Liao Z, Xia X, Zhang Z, Nong B, Guo H, Feng R, Chen C, Xiong F, Qiu Y, Li D, Yang X. Genome-wide association study using specific-locus amplified fragment sequencing identifies new genes influencing nitrogen use efficiency in rice landraces. FRONTIERS IN PLANT SCIENCE 2023; 14:1126254. [PMID: 37521918 PMCID: PMC10375723 DOI: 10.3389/fpls.2023.1126254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 04/28/2023] [Indexed: 08/01/2023]
Abstract
Nitrogen is essential for crop production. It is a critical macronutrient for plant growth and development. However, excessive application of nitrogen fertilizer is not only a waste of resources but also pollutes the environment. An effective approach to solving this problem is to breed rice varieties with high nitrogen use efficiency (NUE). In this study, we performed a genome-wide association study (GWAS) on 419 rice landraces using 208,993 single nucleotide polymorphisms (SNPs). With the mixed linear model (MLM) in the Tassel software, we identified 834 SNPs associated with root surface area (RSA), root length (RL), root branch number (RBN), root number (RN), plant dry weight (PDW), plant height (PH), root volume (RL), plant fresh weight (PFW), root fractal dimension (RFD), number of root nodes (NRN), and average root diameter (ARD), with a significant level of p < 2.39×10-7. In addition, we found 49 SNPs that were correlated with RL, RBN, RN, PDW, PH, PFW, RFD, and NRN using genome-wide efficient mixed-model association (GEMMA), with a significant level of p < 1×10-6. Additionally, the final results for eight traits associated with 193 significant SNPs by using multi-locus random-SNP-effect mixed linear model (mrMLM) model and 272 significant SNPs associated with 11 traits by using IIIVmrMLM. Within the linkage intervals of significantly associated SNP, we identified eight known related genes to NUE in rice, namely, OsAMT2;3, OsGS1, OsNR2, OsNPF7.4, OsPTR9, OsNRT1.1B, OsNRT2.3, and OsNRT2.2. According to the linkage disequilibrium (LD) decay value of this population, there were 75 candidate genes within the 150-kb regions upstream and downstream of the most significantly associated SNP (Chr5_29804690, Chr5_29956584, and Chr10_17540654). These candidate genes included 22 transposon genes, 25 expressed genes, and 28 putative functional genes. The expression levels of these candidate genes were measured by real-time quantitative PCR (RT-qPCR), and the expression levels of LOC_Os05g51700 and LOC_Os05g51710 in C347 were significantly lower than that in C117; the expression levels of LOC_Os05g51740, LOC_Os05g51780, LOC_Os05g51960, LOC_Os05g51970, and LOC_Os10g33210 were significantly higher in C347 than C117. Among them, LOC_Os10g33210 encodes a peptide transporter, and LOC_Os05g51690 encodes a CCT domain protein and responds to NUE in rice. This study identified new loci related to NUE in rice, providing new genetic resources for the molecular breeding of rice landraces with high NUE.
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Affiliation(s)
- Zuyu Liao
- College of Agriculture, Guangxi University, Nanning, China
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Xiuzhong Xia
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Zongqiong Zhang
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Baoxuan Nong
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Hui Guo
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Rui Feng
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Can Chen
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Faqian Xiong
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Yongfu Qiu
- College of Agriculture, Guangxi University, Nanning, China
| | - Danting Li
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Xinghai Yang
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
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12
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Rahmat Z, Sohail MN, Perrine-Walker F, Kaiser BN. Balancing nitrate acquisition strategies in symbiotic legumes. PLANTA 2023; 258:12. [PMID: 37296318 DOI: 10.1007/s00425-023-04175-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 06/01/2023] [Indexed: 06/12/2023]
Abstract
MAIN CONCLUSION Legumes manage both symbiotic (indirect) and non-symbiotic (direct) nitrogen acquisition pathways. Understanding and optimising the direct pathway for nitrate uptake will support greater legume growth and seed yields. Legumes have multiple pathways to acquire reduced nitrogen to grow and set seed. Apart from the symbiotic N2-fixation pathway involving soil-borne rhizobia bacteria, the acquisition of nitrate and ammonia from the soil can also be an important secondary nitrogen source to meet plant N demand. The balance in N delivery between symbiotic N (indirect) and inorganic N uptake (direct) remains less clear over the growing cycle and with the type of legume under cultivation. In fertile, pH balanced agricultural soils, NO3- is often the predominant form of reduced N available to crop plants and will be a major contributor to whole plant N supply if provided at sufficient levels. The transport processes for NO3- uptake into legume root cells and its transport between root and shoot tissues involves both high and low-affinity transport systems called HATS and LATS, respectively. These proteins are regulated by external NO3- availability and by the N status of the cell. Other proteins also play a role in NO3- transport, including the voltage dependent chloride/nitrate channel family (CLC) and the S-type anion channels of the SLAC/SLAH family. CLC's are linked to NO3- transport across the tonoplast of vacuoles and the SLAC/SLAH's with NO3- efflux across the plasma membrane and out of the cell. An important step in managing the N requirements of a plant are the mechanisms involved in root N uptake and the subsequent cellular distribution within the plant. In this review, we will present the current knowledge of these proteins and what is understood on how they function in key model legumes (Lotus japonicus, Medicago truncatula and Glycine sp.). The review will examine their regulation and role in N signalling, discuss how post-translational modification affects NO3- transport in roots and aerial tissues and its translocation to vegetative tissues and storage/remobilization in reproductive tissues. Lastly, we will present how NO3-influences the autoregulation of nodulation and nitrogen fixation and its role in mitigating salt and other abiotic stresses.
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Affiliation(s)
- Zainab Rahmat
- Sydney Institute of Agriculture, The Faculty of Science, University of Sydney, 380 Werombi Road, Brownlow Hill, NSW, 2570, Australia
- School of Natural Sciences, University of Tasmania, Private Bag 55, Hobart, TAS, 7001, Australia
| | - Muhammad N Sohail
- Sydney Institute of Agriculture, The Faculty of Science, University of Sydney, 380 Werombi Road, Brownlow Hill, NSW, 2570, Australia
- School of Natural Sciences, University of Tasmania, Private Bag 55, Hobart, TAS, 7001, Australia
| | - Francine Perrine-Walker
- Sydney Institute of Agriculture, The Faculty of Science, University of Sydney, 380 Werombi Road, Brownlow Hill, NSW, 2570, Australia.
| | - Brent N Kaiser
- Sydney Institute of Agriculture, The Faculty of Science, University of Sydney, 380 Werombi Road, Brownlow Hill, NSW, 2570, Australia.
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Dai S, Wu H, Chen H, Wang Z, Yu X, Wang L, Jia X, Qin C, Zhu Y, Yi K, Zeng H. Comparative transcriptome analyses under individual and combined nutrient starvations provide insights into N/P/K interactions in rice. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 197:107642. [PMID: 36989993 DOI: 10.1016/j.plaphy.2023.107642] [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: 01/04/2023] [Revised: 03/11/2023] [Accepted: 03/13/2023] [Indexed: 06/19/2023]
Abstract
Crops often suffer from simultaneous limitations of multiple nutrients in soils, including nitrogen (N), phosphorus (P) and potassium (K), which are three major macronutrients essential for ensuring growth and yield. Although plant responses to individual N, P, and K deficiency have been well documented, our understanding of the responses to combined nutrient deficiencies and the crosstalk between nutrient starvation responses is still limited. Here, we compared the physiological responses in rice under seven kinds of single and multiple low nutrient stress of N, P and K, and used RNA sequencing approaches to compare their transcriptome changes. A total of 13,000 genes were found to be differentially expressed under all these single and multiple low N/P/K stresses, and 66 and 174 of them were shared by all these stresses in roots and shoots, respectively. Functional enrichment analyses of the DEGs showed that a group of biological and metabolic processes were shared by these low N/P/K stresses. Comparative analyses indicated that DEGs under multiple low nutrient stress was not the simple summation of single nutrient stress. N was found to be the predominant factor affecting the transcriptome under combined nutrient stress. N, P, or K availability exhibited massive influences on the transcriptomic responses to starvation of other nutrients. Many genes involved in nutrient transport, hormone signaling, and transcriptional regulation were commonly responsive to low N/P/K stresses. Some transcription factors were predicted to regulate the expression of genes that are commonly responsive to N, P, and K starvations. These results revealed the interactions between N, P, and K starvation responses, and will be helpful for further elucidation of the molecular mechanisms underlying nutrient interactions.
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Affiliation(s)
- Senhuan Dai
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Haicheng Wu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Huiying Chen
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Zihui Wang
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environment Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xin Yu
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environment Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Long Wang
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xianqing Jia
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Cheng Qin
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Yiyong Zhu
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environment Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Keke Yi
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Houqing Zeng
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China.
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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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15
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Transcriptome and Co-Expression Network Analysis Reveals the Molecular Mechanism of Rice Root Systems in Response to Low-Nitrogen Conditions. Int J Mol Sci 2023; 24:ijms24065290. [PMID: 36982364 PMCID: PMC10048922 DOI: 10.3390/ijms24065290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/03/2023] [Accepted: 03/07/2023] [Indexed: 03/12/2023] Open
Abstract
Nitrogen is an important nutrient for plant growth and essential metabolic processes. Roots integrally obtain nutrients from soil and are closely related to the growth and development of plants. In this study, the morphological analysis of rice root tissues collected at different time points under low-nitrogen and normal nitrogen conditions demonstrated that, compared with normal nitrogen treatment, the root growth and nitrogen use efficiency (NUE) of rice under low-nitrogen treatment were significantly improved. To better understand the molecular mechanisms of the rice root system’s response to low-nitrogen conditions, a comprehensive transcriptome analysis of rice seedling roots under low-nitrogen and control conditions was conducted in this study. As a result, 3171 differentially expressed genes (DEGs) were identified. Rice seedling roots enhance NUE and promote root development by regulating the genes related to nitrogen absorption and utilization, carbon metabolism, root growth and development, and phytohormones, thereby adapting to low-nitrogen conditions. A total of 25,377 genes were divided into 14 modules using weighted gene co-expression network analysis (WGCNA). Two modules were significantly associated with nitrogen absorption and utilization. A total of 8 core genes and 43 co-expression candidates related to nitrogen absorption and utilization were obtained in these two modules. Further studies on these genes will contribute to the understanding of low-nitrogen adaptation and nitrogen utilization mechanisms in rice.
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16
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Alam I, Zhang H, Du H, Rehman NU, Manghwar H, Lei X, Batool K, Ge L. Bioengineering Techniques to Improve Nitrogen Transformation and Utilization: Implications for Nitrogen Use Efficiency and Future Sustainable Crop Production. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:3921-3938. [PMID: 36842151 DOI: 10.1021/acs.jafc.2c08051] [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: 06/18/2023]
Abstract
Nitrogen (N) is crucial for plant growth and development, especially in physiological and biochemical processes such as component of different proteins, enzymes, nucleic acids, and plant growth regulators. Six categories, such as transporters, nitrate absorption, signal molecules, amino acid biosynthesis, transcription factors, and miscellaneous genes, broadly encompass the genes regulating NUE in various cereal crops. Herein, we outline detailed research on bioengineering modifications of N metabolism to improve the different crop yields and biomass. We emphasize effective and precise molecular approaches and technologies, including N transporters, transgenics, omics, etc., which are opening up fascinating opportunities for a complete analysis of the molecular elements that contribute to NUE. Moreover, the detection of various types of N compounds and associated signaling pathways within plant organs have been discussed. Finally, we highlight the broader impacts of increasing NUE in crops, crucial for better agricultural yield and in the greater context of global climate change.
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Affiliation(s)
- Intikhab Alam
- College of Forestry and Landscape Architecture, Department of Grassland Science, South China Agricultural University (SCAU), Guangzhou 510642, China
- College of Life Sciences, SCAU, Guangzhou 510642, China
- Guangdong Subcenter of the National Center for Soybean Improvement, SCAU, Guangzhou 510642, China
| | - Hanyin Zhang
- College of Forestry and Landscape Architecture, Department of Grassland Science, South China Agricultural University (SCAU), Guangzhou 510642, China
- Guangdong Subcenter of the National Center for Soybean Improvement, SCAU, Guangzhou 510642, China
| | - Huan Du
- College of Forestry and Landscape Architecture, Department of Grassland Science, South China Agricultural University (SCAU), Guangzhou 510642, China
- College of Life Sciences, SCAU, Guangzhou 510642, China
- Guangdong Subcenter of the National Center for Soybean Improvement, SCAU, Guangzhou 510642, China
| | - Naveed Ur Rehman
- Guangdong Subcenter of the National Center for Soybean Improvement, SCAU, Guangzhou 510642, China
| | - Hakim Manghwar
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry and Landscape Architecture, SCAU, Guangzhou 510642, China
| | - Xiao Lei
- College of Forestry and Landscape Architecture, Department of Grassland Science, South China Agricultural University (SCAU), Guangzhou 510642, China
- Guangdong Subcenter of the National Center for Soybean Improvement, SCAU, Guangzhou 510642, China
| | - Khadija Batool
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Liangfa Ge
- College of Forestry and Landscape Architecture, Department of Grassland Science, South China Agricultural University (SCAU), Guangzhou 510642, China
- Guangdong Subcenter of the National Center for Soybean Improvement, SCAU, Guangzhou 510642, China
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17
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Choi SJ, Lee Z, Jeong E, Kim S, Seo JS, Um T, Shim JS. Signaling pathways underlying nitrogen transport and metabolism in plants. BMB Rep 2023; 56:56-64. [PMID: 36658636 PMCID: PMC9978367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Indexed: 01/21/2023] Open
Abstract
Nitrogen (N) is an essential macronutrient required for plant growth and crop production. However, N in soil is usually insufficient for plant growth. Thus, chemical N fertilizer has been extensively used to increase crop production. Due to negative effects of N rich fertilizer on the environment, improving N usage has been a major issue in the field of plant science to achieve sustainable production of crops. For that reason, many efforts have been made to elucidate how plants regulate N uptake and utilization according to their surrounding habitat over the last 30 years. Here, we provide recent advances focusing on regulation of N uptake, allocation of N by N transporting system, and signaling pathway controlling N responses in plants. [BMB Reports 2023; 56(2): 56-64].
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Affiliation(s)
- Su Jeong Choi
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Korea
| | - Zion Lee
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Korea
| | - Eui Jeong
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Korea
| | - Sohyun Kim
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Korea
| | - Jun Sung Seo
- Crop Biotechnology Institute, Green Bio Science and Technology, Seoul National University, Pyeongchang 25354, Korea
| | - Taeyoung Um
- Agriculture and Life Sciences Research Institute, Kangwon National University, Chuncheon 24341, Korea
| | - Jae Sung Shim
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Korea,Corresponding author. Tel: +82-62-530-0507; Fax: +82-62-530-2199; E-mail:
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18
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Zhang Y, Fan X, Wang Y, Kong P, Zhao L, Fan X, Zhang Y. OsNAR2.1 induced endogenous nitrogen concentration variation affects transcriptional expression of miRNAs in rice. FRONTIERS IN PLANT SCIENCE 2023; 14:1093676. [PMID: 36909394 PMCID: PMC9998545 DOI: 10.3389/fpls.2023.1093676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 02/13/2023] [Indexed: 06/18/2023]
Abstract
The studies of rice nitrogen concentration on the expression of miRNA so far are mostly limited to the exogenous nitrogen, leaving the effect of endogenous nitrogen largely unexplored. OsNAR2.1 is a high-affinity nitrate transporter partner protein which plays a central role in nitrate absorption and translocation in rice. The expression of OsNAR2.1 could influence the concentration of the endogenous nitrogen in rice. We showed that the expression and production of miRNA in rice can be influenced by manipulating the endogenous nitrogen concentration via OsNAR2.1 transgenic lines. The small RNA content, particularly 24 nucleotides small RNA, expressed differently in two transgenic rice lines (nitrogen efficient line with overexpression of OsNAR2.1 (Ov199), nitrogen-inefficient line with knockdown OsNAR2.1 by RNAi (RNAi)) compared to the wild-type (NP). Comparative hierarchical clustering expression pattern analysis revealed that the expression profiles of mature miRNA in both transgenic lines were different from NP. Several previously unidentified miRNAs were identified to be differentially expressed under different nitrogen concentrations, namely miR1874, miR5150, chr3-36147, chr4-27017 and chr5-21745. In conclusion, our findings suggest that the level of endogenous nitrogen concentration variation by overexpression or knockdown OsNAR2.1 could mediate the expression pattern and intensity of miRNA in rice, which is of high potential to be used in molecular breeding to improve the rice responses towards nitrogen utilization.
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Affiliation(s)
- Yong Zhang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Jiangsu High Quality Rice Research and Development Center, Nanjing Branch of China National Center for Rice Improvement, Nanjing, China
| | - Xiaoru Fan
- School of Chemistry and Life Science, Anshan Normal University, Anshan, China
| | - Yulong Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Pulin Kong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Ling Zhao
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Jiangsu High Quality Rice Research and Development Center, Nanjing Branch of China National Center for Rice Improvement, Nanjing, China
| | - Xiaorong Fan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
- Zhongshan Biological Breeding Laboratory, Nanjing, China
| | - Yadong Zhang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Jiangsu High Quality Rice Research and Development Center, Nanjing Branch of China National Center for Rice Improvement, Nanjing, China
- Zhongshan Biological Breeding Laboratory, Nanjing, China
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19
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Kasemsap P, Bloom AJ. Breeding for Higher Yields of Wheat and Rice through Modifying Nitrogen Metabolism. PLANTS (BASEL, SWITZERLAND) 2022; 12:85. [PMID: 36616214 PMCID: PMC9823454 DOI: 10.3390/plants12010085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/21/2022] [Accepted: 12/21/2022] [Indexed: 06/17/2023]
Abstract
Wheat and rice produce nutritious grains that provide 32% of the protein in the human diet globally. Here, we examine how genetic modifications to improve assimilation of the inorganic nitrogen forms ammonium and nitrate into protein influence grain yield of these crops. Successful breeding for modified nitrogen metabolism has focused on genes that coordinate nitrogen and carbon metabolism, including those that regulate tillering, heading date, and ammonium assimilation. Gaps in our current understanding include (1) species differences among candidate genes in nitrogen metabolism pathways, (2) the extent to which relative abundance of these nitrogen forms across natural soil environments shape crop responses, and (3) natural variation and genetic architecture of nitrogen-mediated yield improvement. Despite extensive research on the genetics of nitrogen metabolism since the rise of synthetic fertilizers, only a few projects targeting nitrogen pathways have resulted in development of cultivars with higher yields. To continue improving grain yield and quality, breeding strategies need to focus concurrently on both carbon and nitrogen assimilation and consider manipulating genes with smaller effects or that underlie regulatory networks as well as genes directly associated with nitrogen metabolism.
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Sinsirimongkol K, Buasong A, Teppabut Y, Pholmanee N, Chen Y, Miller AJ, Punyasuk N. EgNRT2.3 and EgNAR2 expression are controlled by nitrogen deprivation and encode proteins that function as a two-component nitrate uptake system in oil palm. JOURNAL OF PLANT PHYSIOLOGY 2022; 279:153833. [PMID: 36257088 DOI: 10.1016/j.jplph.2022.153833] [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: 11/12/2021] [Revised: 09/29/2022] [Accepted: 10/02/2022] [Indexed: 06/16/2023]
Abstract
Oil palm (Elaeis guineensis Jacq.) is an important crop for oil and biodiesel production. Oil palm plantations require extensive fertilizer additions to achieve a high yield. Fertilizer application decisions and management for oil palm farming rely on leaf tissue and soil nutrient analyses with little information available to describe the key players for nutrient uptake. A molecular understanding of how nutrients, especially nitrogen (N), are taken up in oil palm is very important to improve fertilizer use and formulation practice in oil palm plantations. In this work, two nitrate uptake genes in oil palm, EgNRT2.3 and EgNAR2, were cloned and characterized. Spatial expression analysis showed high expression of these two genes was mainly found in un-lignified young roots. Interestingly, EgNRT2.3 and EgNAR2 were up-regulated by N deprivation, but their expression pattern depended on the form of N source. Promoter analysis of these two genes confirmed the presence of regulatory elements that support these expression patterns. The Xenopus oocyte assay showed that EgNRT2.3 and EgNAR2 had to act together to take up nitrate. The results suggest that EgNRT2.3 and EgNAR2 act as a two-component nitrate uptake system in oil palm.
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Affiliation(s)
| | - Atcharaporn Buasong
- Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Yada Teppabut
- Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Nutthida Pholmanee
- Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Yi Chen
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Anthony J Miller
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Napassorn Punyasuk
- Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.
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Zhang M, Lai L, Liu X, Liu J, Liu R, Wang Y, Liu J, Chen J. Overexpression of Nitrate Transporter 1/Peptide Gene OsNPF7.6 Increases Rice Yield and Nitrogen Use Efficiency. LIFE (BASEL, SWITZERLAND) 2022; 12:life12121981. [PMID: 36556346 PMCID: PMC9786031 DOI: 10.3390/life12121981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/09/2022] [Accepted: 11/11/2022] [Indexed: 11/29/2022]
Abstract
Overuse of nitrogen fertilizer in fields has raised production costs, and caused environmental problems. Improving nitrogen use efficiency (NUE) of rice is essential for sustainable agriculture. Here we report the cloning, characterization and roles for rice of OsNPF7.6, a member of the nitrate transporter 1/peptide transporter family (NPF). The OsNPF7.6 protein is located in the plasma membrane, expressed in each tissue at all stages and is significantly regulated by nitrate in rice. Our study shows that the overexpression of OsNPF7.6 can increase the nitrate uptake rate of rice. Additionally, field experiments showed that OsNPF7.6 overexpression increased the total tiller number per plant and the grain weight per panicle, thereby improving grain yield and agronomic NUE in rice. Thus, OsNPF7.6 can be applied to be a novel target gene for breeding rice varieties with high NUE, and provide a reference for breeding higher yielding rice.
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Affiliation(s)
- Min Zhang
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou 450046, China
| | - Liuru Lai
- School of Agriculture, Shenzhen Campus, Sun Yat-sen University, Shenzhen 518107, China
| | - Xintong Liu
- School of Agriculture, Shenzhen Campus, Sun Yat-sen University, Shenzhen 518107, China
| | - Jiajia Liu
- Shandong Jinchunyu Seed Technology Co., Ltd., Jining 272200, China
| | - Ruifang Liu
- The High School Affiliated to Renmin University of China, Shenzhen 518119, China
| | - Yamei Wang
- School of Agriculture, Shenzhen Campus, Sun Yat-sen University, Shenzhen 518107, China
| | - Jindong Liu
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing 100081, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- Correspondence: (J.L.); (J.C.)
| | - Jingguang Chen
- School of Agriculture, Shenzhen Campus, Sun Yat-sen University, Shenzhen 518107, China
- Correspondence: (J.L.); (J.C.)
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22
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Zhang Y, Tateishi-Karimata H, Endoh T, Jin Q, Li K, Fan X, Ma Y, Gao L, Lu H, Wang Z, Cho AE, Yao X, Liu C, Sugimoto N, Guo S, Fu X, Shen Q, Xu G, Herrera-Estrella LR, Fan X. High-temperature adaptation of an OsNRT2.3 allele is thermoregulated by small RNAs. SCIENCE ADVANCES 2022; 8:eadc9785. [PMID: 36417515 PMCID: PMC9683703 DOI: 10.1126/sciadv.adc9785] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Climate change negatively affects crop yield, which hinders efforts to reach agricultural sustainability and food security. Here, we show that a previously unidentified allele of the nitrate transporter gene OsNRT2.3 is required to maintain high yield and high nitrogen use efficiency under high temperatures. We demonstrate that this tolerance to high temperatures in rice accessions harboring the HTNE-2 (high temperature resistant and nitrogen efficient-2) alleles from enhanced translation of the OsNRT2.3b mRNA isoform and the decreased abundance of a unique small RNA (sNRT2.3-1) derived from the 5' untranslated region of OsNRT2.3. sNRT2.3-1 binds to the OsNRT2.3a mRNA in a temperature-dependent manner. Our findings reveal that allelic variation in the 5' untranslated region of OsNRT2.3 leads to an increase in OsNRT2.3b protein levels and higher yield during high-temperature stress. Our results also provide a breeding strategy to produce rice varieties with higher grain yield and lower N fertilizer input suitable for a sustainable agriculture that is resilient against climate change.
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Affiliation(s)
- Yong Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Hisae Tateishi-Karimata
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Tamaki Endoh
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Qiongli Jin
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Kexin Li
- Department of Bioinformatics, Korea University, Sejong 30019, Republic of Korea
| | - Xiaoru Fan
- School of Chemistry and Life Science, Anshan Normal University, Anshan 114007, China
| | - Yingjun Ma
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Limin Gao
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environment Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Haiyan Lu
- Key Laboratory of Food Quality and Safety of Jiangsu Province, Key Laboratory of Control Technology and Standard for Agro-product Safety and Quality, Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Zhiye Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Art E. Cho
- Department of Bioinformatics, Korea University, Sejong 30019, Republic of Korea
- inCerebro Co. Ltd., 8F Nokmyoung Bldg., 8 Teheran-ro10-gil, Gangnam-gu, Seoul 06234, Republic of Korea
| | - Xuefeng Yao
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Chunming Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100093, China
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
- Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Shiwei Guo
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environment Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiangdong Fu
- 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
| | - Qirong Shen
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environment Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Guohua Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Luis Rafael Herrera-Estrella
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Sciences, Texas Tech University, Lubbock, TX 79409, USA
- Laboratorio Nacional de Genómica para la Biodiversidad, Unidad de Genómica Avanzada del Centro de Investigación yde Estudios Avanzados del Instituto Politécnico Nacional, 36500 Irapuato, Mexico
| | - Xiaorong Fan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
- Corresponding author.
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23
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Saini MR, Chandran LP, Barbadikar KM, Sevanthi AMV, Chawla G, Kaushik M, Mulani E, Phule AS, Govindannagari R, Sonth B, Sinha SK, Sundaram RM, Mandal PK. Understanding plant-microbe interaction of rice and soybean with two contrasting diazotrophic bacteria through comparative transcriptome analysis. FRONTIERS IN PLANT SCIENCE 2022; 13:939395. [PMID: 36483966 PMCID: PMC9724235 DOI: 10.3389/fpls.2022.939395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 10/25/2022] [Indexed: 06/17/2023]
Abstract
Understanding the beneficial plant-microbe interactions is becoming extremely critical for deploying microbes imparting plant fitness and achieving sustainability in agriculture. Diazotrophic bacteria have the unique ability to survive without external sources of nitrogen and simultaneously promote host plant growth, but the mechanisms of endophytic interaction in cereals and legumes have not been studied extensively. We have studied the early interaction of two diazotrophic bacteria, Gluconacetobacter diazotrophicus (GAB) and Bradyrhizobium japonicum (BRH), in 15-day-old seedlings of rice and soybean up to 120 h after inoculation (hai) under low-nitrogen medium. Root colonization of GAB in rice was higher than that of BRH, and BRH colonization was higher in soybean roots as observed from the scanning electron microscopy at 120 hai. Peroxidase enzyme was significantly higher at 24 hai but thereafter was reduced sharply in soybean and gradually in rice. The roots of rice and soybean inoculated with GAB and BRH harvested from five time points were pooled, and transcriptome analysis was executed along with control. Two pathways, "Plant pathogen interaction" and "MAPK signaling," were specific to Rice-Gluconacetobacter (RG), whereas the pathways related to nitrogen metabolism and plant hormone signaling were specific to Rice-Bradyrhizobium (RB) in rice. Comparative transcriptome analysis of the root tissues revealed that several plant-diazotroph-specific differentially expressed genes (DEGs) and metabolic pathways of plant-diazotroph-specific transcripts, viz., chitinase, brassinosteroid, auxin, Myeloblastosis (MYB), nodulin, and nitrate transporter (NRT), were common in all plant-diazotroph combinations; three transcripts, viz., nitrate transport accessory protein (NAR), thaumatin, and thionin, were exclusive in rice and another three transcripts, viz., NAC (NAM: no apical meristem, ATAF: Arabidopsis thaliana activating factor, and CUC: cup-shaped cotyledon), ABA (abscisic acid), and ammonium transporter, were exclusive in soybean. Differential expression of these transcripts and reduction in pathogenesis-related (PR) protein expression show the early interaction. Based on the interaction, it can be inferred that the compatibility of rice and soybean is more with GAB and BRH, respectively. We propose that rice is unable to identify the diazotroph as a beneficial microorganism or a pathogen from an early response. So, it expressed the hypersensitivity-related transcripts along with PR proteins. The molecular mechanism of diazotrophic associations of GAB and BRH with rice vis-à-vis soybean will shed light on the basic understanding of host responses to beneficial microorganisms.
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Affiliation(s)
- Manish Ranjan Saini
- Indian Council of Agricultural Research (ICAR) National Institute for Plant Biotechnology, New Delhi, India
- Kalinga Institute of Industrial Technology (KIIT) School of Biotechnology, KIIT University, Bhubaneswar, India
| | | | | | - Amitha Mithra V. Sevanthi
- Indian Council of Agricultural Research (ICAR) National Institute for Plant Biotechnology, New Delhi, India
| | - Gautam Chawla
- Division of Nematology, ICAR- Indian Agriculture Research Institute, New Delhi, India
| | - Megha Kaushik
- Indian Council of Agricultural Research (ICAR) National Institute for Plant Biotechnology, New Delhi, India
| | - Ekta Mulani
- Indian Council of Agricultural Research (ICAR) National Institute for Plant Biotechnology, New Delhi, India
| | | | | | - Bandeppa Sonth
- ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - Subodh Kumar Sinha
- Indian Council of Agricultural Research (ICAR) National Institute for Plant Biotechnology, New Delhi, India
| | | | - Pranab Kumar Mandal
- Indian Council of Agricultural Research (ICAR) National Institute for Plant Biotechnology, New Delhi, India
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24
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Wang B, Zhou G, Guo S, Li X, Yuan J, Hu A. Improving Nitrogen Use Efficiency in Rice for Sustainable Agriculture: Strategies and Future Perspectives. Life (Basel) 2022; 12:life12101653. [PMID: 36295087 PMCID: PMC9605605 DOI: 10.3390/life12101653] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/29/2022] [Accepted: 10/15/2022] [Indexed: 11/30/2022] Open
Abstract
Nitrogen (N) is an important nutrient for the growth and development of rice. The application of N fertilizer has become one of the inevitable ways to increase rice yield due to insufficient soil N content. However, in order to achieve stable and high yield, farmers usually increase N fertilizer input without hesitation, resulting in a series of problems such as environmental pollution, energy waste and low production efficiency. For sustainable agriculture, improving the nitrogen use efficiency (NUE) to decrease N fertilizer input is imperative. In the present review, we firstly demonstrate the role of N in mediating root architecture, photosynthesis, metabolic balance, and yield components in rice. Furthermore, we further summarize the current agronomic practices for enhancing rice NUE, including balanced fertilization, the use of nitrification inhibitors and slow-release N fertilizers, the split application of N fertilizer, root zone fertilization, and so on. Finally, we discuss the recent advances of N efficiency-related genes with potential breeding value. These genes will contribute to improving the N uptake, maintain the N metabolism balance, and enhance the NUE, thereby breeding new varieties against low N tolerance to improve the rice yield and quality. Moreover, N-efficient varieties also need combine with precise N fertilizer management and advanced cultivation techniques to realize the maximum exploitation of their biological potential.
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Affiliation(s)
- Bo Wang
- Department of Food Crops, Jiangsu Yanjiang Institute of Agricultural Science, Nantong 226012, China
| | - Genyou Zhou
- Department of Food Crops, Jiangsu Yanjiang Institute of Agricultural Science, Nantong 226012, China
| | - Shiyang Guo
- School of Geographic Sciences, Nantong University, Nantong 226019, China
| | - Xiaohui Li
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Jiaqi Yuan
- Department of Food Crops, Jiangsu Yanjiang Institute of Agricultural Science, Nantong 226012, China
| | - Anyong Hu
- School of Geographic Sciences, Nantong University, Nantong 226019, China
- Correspondence:
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25
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OsTBP2.1, a TATA-Binding Protein, Alters the Ratio of OsNRT2.3b to OsNRT2.3a and Improves Rice Grain Yield. Int J Mol Sci 2022; 23:ijms231810795. [PMID: 36142708 PMCID: PMC9503026 DOI: 10.3390/ijms231810795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 09/06/2022] [Accepted: 09/08/2022] [Indexed: 11/30/2022] Open
Abstract
The OsNRT2.3a and OsNRT2.3b isoforms play important roles in the uptake and transport of nitrate during rice growth. However, it is unclear which cis-acting element controls the transcription of OsNRT2.3 into these specific isoforms. In this study, we used a yeast one-hybrid assay to obtain the TATA-box binding protein OsTBP2.1, which binds to the TATA-box of OsNRT2.3, and verified its important role through transient expression and RNA-seq. We found that the TATA-box of OsNRT2.3 mutants and binding protein OsTBP2.1 together increased the transcription ratio of OsNRT2.3b to OsNRT2.3a. The overexpression of OsTBP2.1 promoted nitrogen uptake and increased rice yield compared with the wild-type; however, the OsTBP2.1 T-DNA mutant lines exhibited the opposite trend. Detailed analyses demonstrated that the TATA-box was the key cis-regulatory element for OsNRT2.3 to be transcribed into OsNRT2.3a and OsNRT2.3b. Additionally, this key cis-regulatory element, together with the binding protein OsTBP2.1, promoted the development of rice and increased grain yield.
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26
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Gao Y, Qi S, Wang Y. Nitrate signaling and use efficiency in crops. PLANT COMMUNICATIONS 2022; 3:100353. [PMID: 35754172 PMCID: PMC9483113 DOI: 10.1016/j.xplc.2022.100353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 06/06/2022] [Accepted: 06/23/2022] [Indexed: 06/15/2023]
Abstract
Nitrate (NO3-) is not only an essential nutrient but also an important signaling molecule for plant growth. Low nitrogen use efficiency (NUE) of crops is causing increasingly serious environmental and ecological problems. Understanding the molecular mechanisms of NO3- regulation in crops is crucial for NUE improvement in agriculture. During the last several years, significant progress has been made in understanding the regulation of NO3- signaling in crops, and some key NO3- signaling factors have been shown to play important roles in NO3- utilization. However, no detailed reviews have yet summarized these advances. Here, we focus mainly on recent advances in crop NO3- signaling, including short-term signaling, long-term signaling, and the impact of environmental factors. We also review the regulation of crop NUE by crucial genes involved in NO3- signaling. This review provides useful information for further research on NO3- signaling in crops and a theoretical basis for breeding new crop varieties with high NUE, which has great significance for sustainable agriculture.
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Affiliation(s)
- Yangyang Gao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Shengdong Qi
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Yong Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, China.
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27
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Lv M, Dong T, Wang J, Zuo K. Genome-wide identification of nitrate transporter genes from Spirodela polyrhiza and characterization of SpNRT1.1 function in plant development. FRONTIERS IN PLANT SCIENCE 2022; 13:945470. [PMID: 36061775 PMCID: PMC9436390 DOI: 10.3389/fpls.2022.945470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 07/31/2022] [Indexed: 06/15/2023]
Abstract
Nitrate transporter (NRT) genes that participate in nitrate transport and distribution are indispensable for plant growth, development, and stress tolerance. Spirodela polyrhiza has the smallest genome among monocotyledon plants, and it has strong nitrate absorbance and phytoremediation abilities. However, the evolutionary history, expression patterns, and functions of the NRT gene family in S. polyrhiza are not well understood. Here, we identified 29 NRT members in the S. polyrhiza genome. Gene structure and phylogeny analyses showed that S. polyrhiza nitrate transporter (SpNRTs) genes were divided into eight clades without gene expansion compared with that in Arabidopsis. Transcriptomic analysis showed that SpNRT genes have spatiotemporal expression patterns and respond to abiotic stress. Functional analysis revealed that in S. polyrhiza, SpNRT1.1 expression was strongly induced by treatment with nitrate and ammonium. Overexpression of SpNRT1.1 significantly repressed primary root length, and the number and total length of lateral roots. This was more pronounced in high ammonium concentration medium. Overexpressed SpNRT1.1 in Arabidopsis significantly improved biomass and delayed flowering time, indicating that the nitrate transport ability of SpNRT1.1 differs from AtNRT1.1. In conclusion, our results provide valuable information about the evolution of the NRT family in higher plants and the function of SpNRT1.1.
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Affiliation(s)
- Mengli Lv
- Single Cell Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Tiantian Dong
- Single Cell Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Jin Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Kaijing Zuo
- Single Cell Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
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28
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Shen C, Li Q, An Y, Zhou Y, Zhang Y, He F, Chen L, Liu C, Mao W, Wang X, Liang H, Yin W, Xia X. The transcription factor GNC optimizes nitrogen use efficiency and growth by up-regulating the expression of nitrate uptake and assimilation genes in poplar. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4778-4792. [PMID: 35526197 DOI: 10.1093/jxb/erac190] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 05/05/2022] [Indexed: 06/14/2023]
Abstract
Plants have evolved complex mechanisms to cope with the fluctuating environmental availability of nitrogen. However, potential genes modulating plant responses to nitrate are yet to be characterized. Here, a poplar GATA transcription factor gene PdGNC (GATA nitrate-inducible carbon-metabolism-involved) was found to be strongly induced by low nitrate. Overexpressing PdGNC in poplar clone 717-1B4 (P. tremula × alba) significantly improved nitrate uptake, remobilization, and assimilation with higher nitrogen use efficiency (NUE) and faster growth, particularly under low nitrate conditions. Conversely, CRISPR/Cas9-mediated poplar mutant gnc exhibited decreased nitrate uptake, relocation, and assimilation, combined with lower NUE and slower growth. Assays with yeast one-hybrid, electrophoretic mobility shift, and a dual-luciferase reporter showed that PdGNC directly activated the promoters of nitrogen pathway genes PdNRT2.4b, PdNR, PdNiR, and PdGS2, leading to a significant increase in nitrate utilization in poplar. As expected, the enhanced NUE promoted growth under low nitrate availability. Taken together, our data show that PdGNC plays an important role in the regulation of NUE and growth in poplar by improving nitrate acquisition, remobilization, and assimilation, and provide a promising strategy for molecular breeding to improve productivity under nitrogen limitation in trees.
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Affiliation(s)
- Chao Shen
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Beijing Forestry University, Beijing, China
| | - Qing Li
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Beijing Forestry University, Beijing, China
| | - Yi An
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Beijing Forestry University, Beijing, China
| | - Yangyan Zhou
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Beijing Forestry University, Beijing, China
| | - Yue Zhang
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Beijing Forestry University, Beijing, China
| | - Fang He
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Beijing Forestry University, Beijing, China
| | - Lingyun Chen
- Hangzhou Lifeng Seed Co., Ltd, Hangzhou, Zhejiang 310000, China
| | - Chao Liu
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Beijing Forestry University, Beijing, China
| | - Wei Mao
- Salver Academy of Botany, Rizhao, Shandong 276800, China
| | - Xiaofei Wang
- Salver Academy of Botany, Rizhao, Shandong 276800, China
| | - Haiying Liang
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, USA
| | - Weilun Yin
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Beijing Forestry University, Beijing, China
| | - Xinli Xia
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Beijing Forestry University, Beijing, China
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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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Anandan A, Panda S, Sabarinathan S, Travis AJ, Norton GJ, Price AH. Superior Haplotypes for Early Root Vigor Traits in Rice Under Dry Direct Seeded Low Nitrogen Condition Through Genome Wide Association Mapping. FRONTIERS IN PLANT SCIENCE 2022; 13:911775. [PMID: 35874029 PMCID: PMC9305665 DOI: 10.3389/fpls.2022.911775] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 05/13/2022] [Indexed: 06/14/2023]
Abstract
Water and land resources have been aggressively exploited in the recent decades to meet the growing demands for food. The changing climate has prompted rice scientists and farmers of the tropics and subtropics to adopt the direct seeded rice (DSR) system. DSR system of rice cultivation significantly reduces freshwater consumption and labor requirements, while increasing system productivity, resource use efficiency, and reducing greenhouse gas emissions. Early root vigor is an essential trait required in an ideal DSR system of rice cultivation to ensure a good crop stand, adequate uptake of water, nutrients and compete with weeds. The aus subpopulation which is adapted for DSR was evaluated to understand the biology of early root growth under limited nitrogen conditions over two seasons under two-time points (14 and 28 days). The correlation study identified a positive association between shoot dry weight and root dry weight. The genome-wide association study was conducted on root traits of 14 and 28 days with 2 million single-nucleotide polymorphisms (SNPs) using an efficient mixed model. QTLs over a significant threshold of p < 0.0001 and a 10% false discovery rate were selected to identify genes involved in root growth related to root architecture and nutrient acquisition from 97 QTLs. Candidate genes under these QTLs were explored. On chromosome 4, around 30 Mbp are two important peptide transporters (PTR5 and PTR6) involved in mobilizing nitrogen in the root during the early vegetative stage. In addition, several P transporters and expansin genes with superior haplotypes are discussed. A novel QTL from 21.12 to 21.46 Mb on chromosome 7 with two linkage disequilibrium (LD) blocks governing root length at 14 days were identified. The QTLs/candidate genes with superior haplotype for early root vigor reported here could be explored further to develop genotypes for DSR conditions.
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Affiliation(s)
- Annamalai Anandan
- Crop Improvement Division, Indian Council of Agricultural Research (ICAR)-National Rice Research Institute (NRRI), Cuttack, India
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Seed Science (IISS), Bengaluru, India
| | - Siddharth Panda
- Crop Improvement Division, Indian Council of Agricultural Research (ICAR)-National Rice Research Institute (NRRI), Cuttack, India
- Department of Plant Breeding and Genetics, Odisha University of Agriculture & Technology, Bhubaneswar, India
| | - S. Sabarinathan
- Crop Improvement Division, Indian Council of Agricultural Research (ICAR)-National Rice Research Institute (NRRI), Cuttack, India
| | - Anthony J. Travis
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Gareth J. Norton
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Adam H. Price
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
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31
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Kumar A, Sandhu N, Kumar P, Pruthi G, Singh J, Kaur S, Chhuneja P. Genome-wide identification and in silico analysis of NPF, NRT2, CLC and SLAC1/SLAH nitrate transporters in hexaploid wheat (Triticum aestivum). Sci Rep 2022; 12:11227. [PMID: 35781289 PMCID: PMC9250930 DOI: 10.1038/s41598-022-15202-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 06/20/2022] [Indexed: 11/09/2022] Open
Abstract
Nitrogen transport is one of the most important processes in plants mediated by specialized transmembrane proteins. Plants have two main systems for nitrogen uptake from soil and its transport within the system—a low-affinity transport system and a high-affinity transport system. Nitrate transporters are of special interest in cereal crops because large amount of money is spent on N fertilizers every year to enhance the crop productivity. Till date four gene families of nitrate transporter proteins; NPF (nitrate transporter 1/peptide transporter family), NRT2 (nitrate transporter 2 family), the CLC (chloride channel family), and the SLAC/SLAH (slow anion channel-associated homologues) have been reported in plants. In our study, in silico mining of nitrate transporter genes along with their detailed structure, phylogenetic and expression analysis was carried out. A total of 412 nitrate transporter genes were identified in hexaploid wheat genome using HMMER based homology searches in IWGSC Refseq v2.0. Out of those twenty genes were root specific, 11 leaf/shoot specific and 17 genes were grain/spike specific. The identification of nitrate transporter genes in the close proximity to the previously identified 67 marker-traits associations associated with the nitrogen use efficiency related traits in nested synthetic hexaploid wheat introgression library indicated the robustness of the reported transporter genes. The detailed crosstalk between the genome and proteome and the validation of identified putative candidate genes through expression and gene editing studies may lay down the foundation to improve nitrogen use efficiency of cereal crops.
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Affiliation(s)
- Aman Kumar
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Nitika Sandhu
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, India.
| | - Pankaj Kumar
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Gomsie Pruthi
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Jasneet Singh
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Satinder Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Parveen Chhuneja
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, India
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Chew J, Joseph S, Chen G, Zhang Y, Zhu L, Liu M, Taherymoosavi S, Munroe P, Mitchell DRG, Pan G, Li L, Bian R, Fan X. Biochar-based fertiliser enhances nutrient uptake and transport in rice seedlings. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 826:154174. [PMID: 35231505 DOI: 10.1016/j.scitotenv.2022.154174] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 01/14/2022] [Accepted: 02/23/2022] [Indexed: 06/14/2023]
Abstract
Biochar-based compound fertilisers (BCF) are gaining increasing attention as they are cost-effectiveness and improve soil fertility and crop yield. However, little is known about the mechanisms by which micron-size BCF particles enhance crop growth. In the present study, Wuyunjing7 rice seedlings were exposed to micron-size particles of wheat straw-based BCF (mBCF) diffused through a 25-μm nylon mesh. The control was fertilised with urea, diammonium phosphate, and potassium chloride to ensure that both treatments received comparables level of N, P, and K. The effects of mBCF on rice seedling growth were evaluated by determining the changes in nitrogen uptake and utilisation via nitrogen content measurements, short-term 15N-NH4+ influx assays, and analyses of transcript-level nutrient transporter gene expression. The shoot biomass of rice seedling treated with mBCF at the rate of 5 mg/ g soil was 33% greater than that for the control. Root and shoot 15N accumulation rates were 44% and 14% higher, respectively, in the mBCF-treated than the control. The mBCF-treated rice seedlings had higher phosphorus, potassium, and iron content than the control. Moreover, the treatments significantly differed in terms of their nutrient transporter gene expression levels. Spectroscopy and microscopy were used to visualise nutrient distributions across transverse root sections. There were relatively higher iron oxide nanoparticle and silicon-based compound concentrations in the roots of the mBCF-treated rice seedlings than in those of the control. The foregoing difference might account for the fact that the growth of the mBCF-treated rice was superior to that of the control. We demonstrated that the mBCF treatment created a more negative electrical potential at the root epidermal cell layer (~ - 160 mV) than the root surface. This potential difference may have been the driving force for mineral nutrient absorption.
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Affiliation(s)
- JinKiat Chew
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Stephen Joseph
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China; School of Materials Science and Engineering, University of NSW, Sydney, NSW 2052, Australia; Institute for Superconducting and Electronic Materials and School of Physics, University of Wollongong, NSW 2522, Australia
| | - Guanhong Chen
- Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Yuyue Zhang
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Longlong Zhu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Minglong Liu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | | | - Paul Munroe
- School of Materials Science and Engineering, University of NSW, Sydney, NSW 2052, Australia
| | - David R G Mitchell
- Electron Microscopy Centre, AIIM Building, Innovation Campus, University of Wollongong, North Wollongong, NSW 2517, Australia
| | - Genxing Pan
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Lianqing Li
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Rongjun Bian
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaorong Fan
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
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Carillo P, Rouphael Y. Nitrate Uptake and Use Efficiency: Pros and Cons of Chloride Interference in the Vegetable Crops. FRONTIERS IN PLANT SCIENCE 2022; 13:899522. [PMID: 35783949 PMCID: PMC9244799 DOI: 10.3389/fpls.2022.899522] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 05/20/2022] [Indexed: 05/29/2023]
Abstract
Over the past five decades, nitrogen (N) fertilization has been an essential tool for boosting crop productivity in agricultural systems. To avoid N pollution while preserving the crop yields and profit margins for farmers, the scientific community is searching for eco-sustainable strategies aimed at increasing plants' nitrogen use efficiency (NUE). The present article provides a refined definition of the NUE based on the two important physiological factors (N-uptake and N-utilization efficiency). The diverse molecular and physiological mechanisms underlying the processes of N assimilation, translocation, transport, accumulation, and reallocation are revisited and critically discussed. The review concludes by examining the N uptake and NUE in tandem with chloride stress and eustress, the latter being a new approach toward enhancing productivity and functional quality of the horticultural crops, particularly facilitated by soilless cultivation.
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Affiliation(s)
- Petronia Carillo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania Luigi Vanvitelli, Caserta, Italy
| | - Youssef Rouphael
- Department of Agricultural Sciences, University of Naples Federico II, Naples, Italy
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34
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Pachamuthu K, Hari Sundar V, Narjala A, Singh RR, Das S, Avik Pal HCY, Shivaprasad PV. Nitrate-dependent regulation of miR444-OsMADS27 signalling cascade controls root development in rice. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:3511-3530. [PMID: 35243491 DOI: 10.1093/jxb/erac083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 03/02/2022] [Indexed: 06/14/2023]
Abstract
Nitrate is an important nutrient and a key signalling molecule for plant development. A number of transcription factors involved in the response to nitrate and their regulatory mechanisms have been identified. However, little is known about the transcription factors involved in nitrate sensing and their regulatory mechanisms among crop plants. In this study, we identified functions of a nitrate-responsive miR444:MADS-box transcription factor OsMADS27 module and its downstream targets mediating rice root growth and stress responses. Transgenic rice plants expressing miR444 target mimic improved rice root growth. Although miR444 has the potential to target multiple genes, we identified OsMADS27 as the major miR444 target that regulates the expression of nitrate transporters, as well as several key genes including expansins, and those associated with auxin signalling, to promote root growth. In agreement with this, overexpression of miRNA-resistant OsMADS27 improved root development and tolerance to abiotic stresses, while its silencing suppressed root growth. OsMADS27 mediated robust stress tolerance in plants through its ability to bind to the promoters of specific stress regulators, as observed in ChIP-seq analysis. Our results provide evidence of a nitrate-dependent miR444-OsMADS27 signalling cascade involved in the regulation of rice root growth, as well as its surprising role in stress responses.
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Affiliation(s)
- Kannan Pachamuthu
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, India
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris- Saclay, Versailles, France
| | - Vivek Hari Sundar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, India
| | - Anushree Narjala
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, India
- SASTRA University, Thirumalaisamudram, Thanjavur, India
| | - Rahul R Singh
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, India
- Department of Biological Sciences, North Dakota State University, Fargo, ND, USA
| | - Soumita Das
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, India
| | - Harshith C Y Avik Pal
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, India
| | - Padubidri V Shivaprasad
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, India
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35
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Liu Q, Wu K, Song W, Zhong N, Wu Y, Fu X. Improving Crop Nitrogen Use Efficiency Toward Sustainable Green Revolution. ANNUAL REVIEW OF PLANT BIOLOGY 2022; 73:523-551. [PMID: 35595292 DOI: 10.1146/annurev-arplant-070121-015752] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The Green Revolution of the 1960s improved crop yields in part through the widespread cultivation of semidwarf plant varieties, which resist lodging but require a high-nitrogen (N) fertilizer input. Because environmentally degrading synthetic fertilizer use underlies current worldwide cereal yields, future agricultural sustainability demands enhanced N use efficiency (NUE). Here, we summarize the current understanding of how plants sense, uptake, and respond to N availability in the model plants that can be used to improve sustainable productivity in agriculture. Recent progress in unlocking the genetic basis of NUE within the broader context of plant systems biology has provided insights into the coordination of plant growth and nutrient assimilation and inspired the implementation of a new breeding strategy to cut fertilizer use in high-yield cereal crops. We conclude that identifying fresh targets for N sensing and response in crops would simultaneously enable improved grain productivity and NUE to launch a new Green Revolution and promote future food security.
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Affiliation(s)
- Qian Liu
- 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, China;
| | - Kun Wu
- 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, China;
| | - Wenzhen Song
- 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, China;
| | - Nan Zhong
- 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, China;
| | - Yunzhe Wu
- 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, China;
| | - Xiangdong Fu
- 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, China;
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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36
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Zhang ZS, Xia JQ, Alfatih A, Song Y, Huang YJ, Sun LQ, Wan GY, Wang SM, Wang YP, Hu BH, Zhang GH, Qin P, Li SG, Yu LH, Wu J, Xiang CB. Rice NIN-LIKE PROTEIN 3 modulates nitrogen use efficiency and grain yield under nitrate-sufficient conditions. PLANT, CELL & ENVIRONMENT 2022; 45:1520-1536. [PMID: 35150141 DOI: 10.1111/pce.14294] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/27/2022] [Accepted: 01/31/2022] [Indexed: 06/14/2023]
Abstract
Nitrogen (N) is an essential macronutrient for crop growth and yield. Improving the N use efficiency (NUE) of crops is important to agriculture. However, the molecular mechanisms underlying NUE regulation remain largely elusive. Here we report that the OsNLP3 (NIN-like protein 3) regulates NUE and grain yield in rice under N sufficient conditions. OsNLP3 transcript level is significantly induced by N starvation and its protein nucleocytosolic shuttling is specifically regulated by nitrate. Loss-of-function of OsNLP3 reduces plant growth, grain yield, and NUE under sufficient nitrate conditions, whereas under low nitrate or different ammonium conditions, osnlp3 mutants show no clear difference from the wild type. Importantly, under sufficient N conditions in the field, OsNLP3 overexpression lines display improved grain yield and NUE compared with the wild type. OsNLP3 orchestrates the expression of multiple N uptake and assimilation genes by directly binding to the nitrate-responsive cis-elements in their promoters. Overall, our study demonstrates that OsNLP3, together with OsNLP1 and OsNLP4, plays overlapping and differential roles in N acquisition and NUE, and modulates NUE and the grain yield increase promoted by N fertilizer. Therefore, OsNLP3 is a promising candidate gene for the genetic improvement of grain yield and NUE in rice.
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Affiliation(s)
- Zi-Sheng Zhang
- School of Life Sciences, Division of Molecular & Cell Biophysics, Hefei National Science Center for Physical Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, China
| | - Jin-Qiu Xia
- School of Life Sciences, Division of Molecular & Cell Biophysics, Hefei National Science Center for Physical Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, China
| | - Alamin Alfatih
- School of Life Sciences, Division of Molecular & Cell Biophysics, Hefei National Science Center for Physical Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, China
| | - Ying Song
- School of Life Sciences, Division of Molecular & Cell Biophysics, Hefei National Science Center for Physical Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, China
| | - Yi-Jie Huang
- School of Life Sciences, Division of Molecular & Cell Biophysics, Hefei National Science Center for Physical Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, China
| | - Liang-Qi Sun
- School of Life Sciences, Division of Molecular & Cell Biophysics, Hefei National Science Center for Physical Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, China
| | - Guang-Yu Wan
- School of Life Sciences, Division of Molecular & Cell Biophysics, Hefei National Science Center for Physical Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, China
| | - Shi-Mei Wang
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Yu-Ping Wang
- Rice Research Institute, State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, China
| | - Bin-Hua Hu
- Rice Research Institute, State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, China
| | - Guo-Hua Zhang
- Rice Research Institute, State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, China
| | - Peng Qin
- Rice Research Institute, State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, China
| | - Shi-Gui Li
- Rice Research Institute, State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, China
| | - Lin-Hui Yu
- School of Life Sciences, Division of Molecular & Cell Biophysics, Hefei National Science Center for Physical Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, China
- State Key Laboratory of Crop Stress Biology for Arid Areas and Institute of Future Agriculture, Northwest A&F University, Yangling, Shanxi, China
| | - Jie Wu
- School of Life Sciences, Division of Molecular & Cell Biophysics, Hefei National Science Center for Physical Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, China
| | - Cheng-Bin Xiang
- School of Life Sciences, Division of Molecular & Cell Biophysics, Hefei National Science Center for Physical Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, China
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McDonald TR, Rizvi MF, Ruiter BL, Roy R, Reinders A, Ward JM. Posttranslational regulation of transporters important for symbiotic interactions. PLANT PHYSIOLOGY 2022; 188:941-954. [PMID: 34850211 PMCID: PMC8825328 DOI: 10.1093/plphys/kiab544] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 10/27/2021] [Indexed: 05/20/2023]
Abstract
Coordinated sharing of nutritional resources is a central feature of symbiotic interactions, and, despite the importance of this topic, many questions remain concerning the identification, activity, and regulation of transporter proteins involved. Recent progress in obtaining genome and transcriptome sequences for symbiotic organisms provides a wealth of information on plant, fungal, and bacterial transporters that can be applied to these questions. In this update, we focus on legume-rhizobia and mycorrhizal symbioses and how transporters at the symbiotic interfaces can be regulated at the protein level. We point out areas where more research is needed and ways that an understanding of transporter mechanism and energetics can focus hypotheses. Protein phosphorylation is a predominant mechanism of posttranslational regulation of transporters in general and at the symbiotic interface specifically. Other mechanisms of transporter regulation, such as protein-protein interaction, including transporter multimerization, polar localization, and regulation by pH and membrane potential are also important at the symbiotic interface. Most of the transporters that function in the symbiotic interface are members of transporter families; we bring in relevant information on posttranslational regulation within transporter families to help generate hypotheses for transporter regulation at the symbiotic interface.
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Affiliation(s)
- Tami R McDonald
- Department of Biology, St Catherine University, St Paul, Minnesota, USA
| | - Madeeha F Rizvi
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
| | - Bretton L Ruiter
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
| | - Rahul Roy
- Department of Biology, St Catherine University, St Paul, Minnesota, USA
| | - Anke Reinders
- College of Continuing and Professional Studies, University of Minnesota, St. Paul, Minnesota, USA
| | - John M Ward
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
- Author for communication:
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38
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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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New insights into the role of chrysanthemum calcineurin B-like interacting protein kinase CmCIPK23 in nitrate signaling in Arabidopsis roots. Sci Rep 2022; 12:1018. [PMID: 35046428 PMCID: PMC8770472 DOI: 10.1038/s41598-021-04758-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 12/30/2021] [Indexed: 02/07/2023] Open
Abstract
Nitrate is an important source of nitrogen and also acts as a signaling molecule to trigger numerous physiological, growth, and developmental processes throughout the life of the plant. Many nitrate transporters, transcription factors, and protein kinases participate in the regulation of nitrate signaling. Here, we identified a gene encoding the chrysanthemum calcineurin B-like interacting protein kinase CmCIPK23, which participates in nitrate signaling pathways. In Arabidopsis, overexpression of CmCIPK23 significantly decreased lateral root number and length and primary root length compared to the WT when grown on modified Murashige and Skoog medium with KNO3 as the sole nitrogen source (modified MS). The expression of nitrate-responsive genes differed significantly between CmCIPK23-overexpressing Arabidopsis (CmCIPK23-OE) and the WT after nitrate treatment. Nitrate content was significantly lower in CmCIPK23-OE roots, which may have resulted from reduced nitrate uptake at high external nitrate concentrations (≥ 1 mM). Nitrate reductase activity and the expression of nitrate reductase and glutamine synthase genes were lower in CmCIPK23-OE roots. We also found that CmCIPK23 interacted with the transcription factor CmTGA1, whose Arabidopsis homolog regulates the nitrate response. We inferred that CmCIPK23 overexpression influences root development on modified MS medium, as well as root nitrate uptake and assimilation at high external nitrate supply. These findings offer new perspectives on the mechanisms by which the chrysanthemum CBL interacting protein kinase CmCIPK23 influences nitrate signaling.
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Ji C, Li J, Jiang C, Zhang L, Shi L, Xu F, Cai H. Zinc and nitrogen synergistic act on root-to-shoot translocation and preferential distribution in rice. J Adv Res 2022; 35:187-198. [PMID: 35003800 PMCID: PMC8721242 DOI: 10.1016/j.jare.2021.04.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 04/06/2021] [Accepted: 04/15/2021] [Indexed: 11/30/2022] Open
Abstract
Zn promoted translocation and distribution of N into leaves and brown rice. Zn induced the expression levels of N transporter genes in both root and shoot. Zn increased the N assimilation level in leaves. N promoted translocation and distribution of Zn into leaves and brown rice. N up-regulated the expression levels of Zn transporter genes in both root and shoot.
Introduction Multiple studies have shown strong relationships between different nutrients in plants, and the important role of N in Zn acquisition and translocation has been recognized. Objectives The aim of this study was to estimate the effect of Zn on N uptake, translocation, and distribution in rice as well as the corresponding molecular mechanisms. We also aimed to evaluate the impact of N on the Zn content in rice grains which is closely related to the Zn nutrition in humans with rice-based diets. Methods We conducted both field trials and hydroponic cultures of two rice cultivars to analyze the growth and yield, the uptake, translocation, and distribution of N and Zn, as well as the expression of N transport and assimilation genes, and the Zn transporter genes under different combined applications of N and Zn. Results Zn supply promoted the root-to-shoot translocation (12–70% increasing) and distribution of N into the leaves (19–49% increasing) and brown rice (6–9% increasing) and increased the rice biomass (by 14–35%) and yield (by 13–63%). Zn supply induced the expression of OsNRTs and OsAMTs in both roots and shoots, but repressed the expression of OsNiR2, OsGS1;2, and OsFd-GOGAT in roots, whereas it activated the expression of OsNiR2, OsGS1;1, OsGS2, and OsFd-GOGAT in the shoots. Moreover, the enzyme activities of nitrite reductase, nitrate reductase, and glutamine synthetase increased and the free NO3– concentration decreased, but the soluble protein concentration increased significantly in the shoots after Zn supply. Synergistically, N significantly facilitated the root-to-shoot translocation (1.68–11.66 fold) and distribution of Zn into the leaves (1.68–6.37 fold) and brown rice (7–12% increasing) and upregulated the expression levels of Zn transporter genes in both the roots and shoots. Conclusions We propose a working model of the cross-talk between Zn and N in rice plants, which will aid in the appropriate combined application of Zn and N fertilizers in the field to improve both N utilization in plants and Zn nutrition in humans with rice-based diets.
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Key Words
- AMT, ammonium transporter
- Distribution
- GLY, Guangliangyou 35
- GOGAT, glutamate synthase
- GS, glutamine synthetase
- Interaction
- N, nitrogen
- NR, nitrate reductase
- NRT, nitrate transporter
- NiR, nitrite reductase
- Nip, Nipponbare
- Nitrogen
- Rice
- Translocation
- ZIP, ZRT, IRT-like protein
- Zinc
- Zn, Zinc
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Affiliation(s)
- Chenchen Ji
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Junli Li
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Cuncang Jiang
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Lin Zhang
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Lei Shi
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
- National Key Laboratory of Crop Genetics and Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Fangsen Xu
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
- National Key Laboratory of Crop Genetics and Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Hongmei Cai
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
- Corresponding author.
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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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Sandhu N, Pruthi G, Prakash Raigar O, Singh MP, Phagna K, Kumar A, Sethi M, Singh J, Ade PA, Saini DK. Meta-QTL Analysis in Rice and Cross-Genome Talk of the Genomic Regions Controlling Nitrogen Use Efficiency in Cereal Crops Revealing Phylogenetic Relationship. Front Genet 2021; 12:807210. [PMID: 34992638 PMCID: PMC8724540 DOI: 10.3389/fgene.2021.807210] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 11/30/2021] [Indexed: 11/13/2022] Open
Abstract
The phenomenal increase in the use of nitrogenous fertilizers coupled with poor nitrogen use efficiency is among the most important threats to the environment, economic, and social health. During the last 2 decades, a number of genomic regions associated with nitrogen use efficiency (NUE) and related traits have been reported by different research groups, but none of the stable and major effect QTL have been utilized in the marker-assisted introgression/pyramiding program. Compiling the data available in the literature could be very useful in identifying stable and major effect genomic regions associated with the root and NUE-related trait improving the rice grain yield. In the present study, we performed meta-QTL analysis on 1,330 QTL from 29 studies published in the past 2 decades. A total of 76 MQTL with a stable effect over different genetic backgrounds and environments were identified. The significant reduction in the confidence interval of the MQTL compared to the initial QTL resulted in the identification of annotated and putative candidate genes related to the traits considered in the present study. A hot spot region associated with correlated traits on chr 1, 4, and 8 and candidate genes associated with nitrate transporters, nitrogen content, and ammonium uptake on chromosomes 2, 4, 6, and 8 have been identified. The identified MQTL, putative candidate genes, and their orthologues were validated on our previous studies conducted on rice and wheat. The research-based interventions such as improving nitrogen use efficiency via identification of major genomic regions and candidate genes can be a plausible, simple, and low-cost solution to address the challenges of the crop improvement program.
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Affiliation(s)
| | | | | | | | - Kanika Phagna
- Indian Institute of Science Education and Research, Berhampur, India
| | - Aman Kumar
- Punjab Agricultural University, Ludhiana, India
| | - Mehak Sethi
- Punjab Agricultural University, Ludhiana, India
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Lebedev VG, Popova AA, Shestibratov KA. Genetic Engineering and Genome Editing for Improving Nitrogen Use Efficiency in Plants. Cells 2021; 10:cells10123303. [PMID: 34943810 PMCID: PMC8699818 DOI: 10.3390/cells10123303] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/18/2021] [Accepted: 11/23/2021] [Indexed: 12/15/2022] Open
Abstract
Low nitrogen availability is one of the main limiting factors for plant growth and development, and high doses of N fertilizers are necessary to achieve high yields in agriculture. However, most N is not used by plants and pollutes the environment. This situation can be improved by enhancing the nitrogen use efficiency (NUE) in plants. NUE is a complex trait driven by multiple interactions between genetic and environmental factors, and its improvement requires a fundamental understanding of the key steps in plant N metabolism—uptake, assimilation, and remobilization. This review summarizes two decades of research into bioengineering modification of N metabolism to increase the biomass accumulation and yield in crops. The expression of structural and regulatory genes was most often altered using overexpression strategies, although RNAi and genome editing techniques were also used. Particular attention was paid to woody plants, which have great economic importance, play a crucial role in the ecosystems and have fundamental differences from herbaceous species. The review also considers the issue of unintended effects of transgenic plants with modified N metabolism, e.g., early flowering—a research topic which is currently receiving little attention. The future prospects of improving NUE in crops, essential for the development of sustainable agriculture, using various approaches and in the context of global climate change, are discussed.
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Affiliation(s)
- Vadim G. Lebedev
- Forest Biotechnology Group, Branch of the Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 142290 Pushchino, Russia;
- Correspondence:
| | - Anna A. Popova
- Department of Botany and Plant Physiology, Voronezh State University of Forestry and Technologies named after G.F. Morozov, 394087 Voronezh, Russia;
| | - Konstantin A. Shestibratov
- Forest Biotechnology Group, Branch of the Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 142290 Pushchino, Russia;
- Department of Botany and Plant Physiology, Voronezh State University of Forestry and Technologies named after G.F. Morozov, 394087 Voronezh, Russia;
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Cheng P, Wang J, Zhao Z, Kong L, Lou W, Zhang T, Jing D, Yu J, Shu Z, Huang L, Zhu W, Yang Q, Shen W. Molecular Hydrogen Increases Quantitative and Qualitative Traits of Rice Grain in Field Trials. PLANTS (BASEL, SWITZERLAND) 2021; 10:2331. [PMID: 34834694 PMCID: PMC8624507 DOI: 10.3390/plants10112331] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 10/24/2021] [Accepted: 10/26/2021] [Indexed: 06/13/2023]
Abstract
How to use environmentally friendly technology to enhance rice field and grain quality is a challenge for the scientific community. Here, we showed that the application of molecular hydrogen in the form of hydrogen nanobubble water could increase the length, width, and thickness of brown/rough rice and white rice, as well as 1000-grain weight, compared to the irrigation with ditch water. The above results were well matched with the transcriptional profiles of representative genes related to high yield, including up-regulation of heterotrimeric G protein β-subunit gene (RGB1) for cellular proliferation, Grain size 5 (GS5) for grain width, Small grain 1 (SMG1) for grain length and width, Grain weight 8 (GW8) for grain width and weight, and down-regulation of negatively correlated gene Grain size 3 (GS3) for grain length. Meanwhile, although total starch content in white rice is not altered by HNW, the content of amylose was decreased by 31.6%, which was parallel to the changes in the transcripts of the amylose metabolism genes. In particular, cadmium accumulation in white rice was significantly reduced, reaching 52% of the control group. This phenomenon was correlated well with the differential expression of transporter genes responsible for Cd entering plants, including down-regulated Natural resistance-associated macrophage protein (Nramp5), Heavy metal transporting ATPase (HMA2 and HMA3), and Iron-regulated transporters (IRT1), and for decreasing Cd accumulation in grain, including down-regulated Low cadmium (LCD). This study clearly showed that the application of molecular hydrogen might be used as an effective approach to increase field and grain quality of rice.
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Affiliation(s)
- Pengfei Cheng
- Laboratory Center of Life Sciences, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (P.C.); (J.W.); (Z.Z.); (L.K.); (W.L.); (T.Z.); (W.Z.); (Q.Y.)
| | - Jun Wang
- Laboratory Center of Life Sciences, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (P.C.); (J.W.); (Z.Z.); (L.K.); (W.L.); (T.Z.); (W.Z.); (Q.Y.)
| | - Zhushan Zhao
- Laboratory Center of Life Sciences, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (P.C.); (J.W.); (Z.Z.); (L.K.); (W.L.); (T.Z.); (W.Z.); (Q.Y.)
| | - Lingshuai Kong
- Laboratory Center of Life Sciences, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (P.C.); (J.W.); (Z.Z.); (L.K.); (W.L.); (T.Z.); (W.Z.); (Q.Y.)
| | - Wang Lou
- Laboratory Center of Life Sciences, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (P.C.); (J.W.); (Z.Z.); (L.K.); (W.L.); (T.Z.); (W.Z.); (Q.Y.)
| | - Tong Zhang
- Laboratory Center of Life Sciences, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (P.C.); (J.W.); (Z.Z.); (L.K.); (W.L.); (T.Z.); (W.Z.); (Q.Y.)
| | - Dedao Jing
- Zhenjiang Institute of Agricultural Science of the Ning-Zhen Hilly District, Jurong 212400, China; (D.J.); (J.Y.); (Z.S.)
| | - Julong Yu
- Zhenjiang Institute of Agricultural Science of the Ning-Zhen Hilly District, Jurong 212400, China; (D.J.); (J.Y.); (Z.S.)
| | - Zhaolin Shu
- Zhenjiang Institute of Agricultural Science of the Ning-Zhen Hilly District, Jurong 212400, China; (D.J.); (J.Y.); (Z.S.)
| | - Liqin Huang
- College of Sciences, Nanjing Agricultural University, Nanjing 210095, China;
| | - Wenjiao Zhu
- Laboratory Center of Life Sciences, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (P.C.); (J.W.); (Z.Z.); (L.K.); (W.L.); (T.Z.); (W.Z.); (Q.Y.)
| | - Qing Yang
- Laboratory Center of Life Sciences, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (P.C.); (J.W.); (Z.Z.); (L.K.); (W.L.); (T.Z.); (W.Z.); (Q.Y.)
| | - Wenbiao Shen
- Laboratory Center of Life Sciences, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (P.C.); (J.W.); (Z.Z.); (L.K.); (W.L.); (T.Z.); (W.Z.); (Q.Y.)
- Center of Hydrogen Science, Shanghai Jiao Tong University, Shanghai 200240, China
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Islam MQ, Hasan MN, Hoque H, Jewel NA, Bhuiyan MFH, Prodhan SH. Characterization of transcription factor MYB59 and expression profiling in response to low K + and NO 3- in indica rice (Oryza sativa L.). J Genet Eng Biotechnol 2021; 19:167. [PMID: 34704216 PMCID: PMC8548439 DOI: 10.1186/s43141-021-00248-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 09/18/2021] [Indexed: 11/11/2022]
Abstract
Background Nitrogen and potassium are crucial supplements for plant development and growth. Plants can detect potassium and nitrate ions in soils and in like way, they modify root-to-shoot transport of these ions to adjust the conveyance among roots and shoots. Transcription factor MYB59 plays essential roles in numerous physiological processes inclusive of hormone response, abiotic stress tolerance, plant development, and metabolic regulation. In this study, we retrieved 56 MYB59 proteins from different plant species. Multiple sequence alignment, phylogenetic tree, conserved motif, chromosomal localization, and cis-regulatory elements of the retrieved sequences were analyzed. Gene structure, protein 3D structure, and DNA binding of OsMYB59 indica were also predicted. Finally, we characterized OsMYB59 and its function under low K+/NO3− conditions in Oryza sativa subsp. indica. Results Data analysis showed that MYB59s from various groups separated in terms of conserved functional domains and gene structure, where members of genus Oryza clustered together. Plants showed reduced height and yellowish appearance when grown on K+ and NO3− deficient medium. Quantitative real-time PCR uncovered that the OsMYB59 reacted to abiotic stresses where its expression was increased in BRRI dhan56 but decreased in other varieties on K+ deficient medium. In addition, OsMYB59 transcript level increased on NO3− deficient medium. Conclusions Our results can help to explain the biological functions of indica rice MYB59 protein and gave a theoretical premise to additionally describe its biological roles in response to abiotic stresses particularly drought. Supplementary Information The online version contains supplementary material available at 10.1186/s43141-021-00248-6.
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Affiliation(s)
- Md Qamrul Islam
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Md Nazmul Hasan
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Hammadul Hoque
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Nurnabi Azad Jewel
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Md Fahmid Hossain Bhuiyan
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Shamsul H Prodhan
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh.
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Transporters and transcription factors gene families involved in improving nitrogen use efficiency (NUE) and assimilation in rice (Oryza sativa L.). Transgenic Res 2021; 31:23-42. [PMID: 34524604 DOI: 10.1007/s11248-021-00284-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 09/06/2021] [Indexed: 12/18/2022]
Abstract
Nitrogen (N) as a macronutrient is an important determinant of plant growth. The excessive usage of chemical fertilizers is increasing environmental pollution; hence, the improvement of crop's nitrogen use efficiency (NUE) is imperative for sustainable agriculture. N uptake, transportation, assimilation, and remobilization are four important determinants of plant NUE. Oryza sativa L. (rice) is a staple food for approximately half of the human population, around the globe and improvement in rice yield is pivotal for rice breeders. The N transporters, enzymes indulged in N assimilation, and several transcription factors affect the rice NUE and subsequent yield. Although, a couple of improvements have been made regarding rice NUE, the knowledge about regulatory mechanisms operating NUE is scarce. The current review provides a precise knowledge of how rice plants detect soil N and how this detection is translated into the language of responses that regulate the growth. Additionally, the transcription factors that control N-associated genes in rice are discussed in detail. This mechanistic insight will help the researchers to improve rice yield with minimized use of chemical fertilizers.
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Xiang J, Qian K, Zhang Y, Chew J, Liang J, Zhu J, Zhang Y, Fan X. OsLSD1.1 is involved in the photosystem II reaction and affects nitrogen allocation in rice. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 166:246-257. [PMID: 34126592 DOI: 10.1016/j.plaphy.2021.06.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 06/03/2021] [Indexed: 05/20/2023]
Abstract
Nitrogen (N) is an essential nutrient element for plants; however, high N accumulation often leads to a decrease in photosynthetic nitrogen use efficiency (PNUE). In rice (Oryza sativa L.), well-developed aerenchyma is formed to promote oxygen transport from the shoot to the root tips as an adaptation to submerged and oxygen-deficient environment. Total N concentrations were increased in the rice root by changes in O2 levels in the rhizosphere. However, few reports have focused on how aerenchyma formation-related genes participate in photosynthesis and affect nitrogen allocation in rice. In this study, we found that OsLSD1.1, located in the chloroplast, cell membrane, and nucleus, may be involved in the photosystem II reaction and affect chloroplast development. OsLSD1.1 knockout was found to significantly reduce the quantum efficiency of the PSII reaction center (ΦPSII). Furthermore, we observed that the nitrogen accumulation decreased in the grain of OsLSD1.1 mutants. RNA-Seq transcriptome analysis revealed that OsPEPC3, OsPsbR1, OsNRG2, OsNRT1.5A, OsNRT1.7, and OsAMT3;2 were downregulated in m12 compared with N-WT (wild-type Nipponbare), which may be a reason that photosynthesis and nitrogen transport were inhibited. Taken together, our findings demonstrated that OsLSD1.1 may be key in plant growth, photosynthesis, and nitrogen allocation in rice. Our results may provide theoretical support for the discovery of key genes for nitrogen physiological use efficiency.
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Affiliation(s)
- Jinxia Xiang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China; Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Kaiyun Qian
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China; Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Yuyue Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China; Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Jinkiat Chew
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China; Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Jing Liang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Jingwen Zhu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Yong Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China; Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Xiaorong Fan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China; Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China.
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Molecular Regulatory Networks for Improving Nitrogen Use Efficiency in Rice. Int J Mol Sci 2021; 22:ijms22169040. [PMID: 34445746 PMCID: PMC8396546 DOI: 10.3390/ijms22169040] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/15/2021] [Accepted: 08/17/2021] [Indexed: 11/17/2022] Open
Abstract
Nitrogen is an important factor limiting the growth and yield of rice. However, the excessive application of nitrogen will lead to water eutrophication and economic costs. To create rice varieties with high nitrogen use efficiency (NUE) has always been an arduous task in rice breeding. The processes for improving NUE include nitrogen uptake, nitrogen transport from root to shoot, nitrogen assimilation, and nitrogen redistribution, with each step being indispensable to the improvement of NUE. Here, we summarize the effects of absorption, transport, and metabolism of nitrate, ammonium, and amino acids on NUE, as well as the role of hormones in improving rice NUE. Our discussion provide insight for further research in the future.
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Liang T, Yuan Z, Fu L, Zhu M, Luo X, Xu W, Yuan H, Zhu R, Hu Z, Wu X. Integrative Transcriptomic and Proteomic Analysis Reveals an Alternative Molecular Network of Glutamine Synthetase 2 Corresponding to Nitrogen Deficiency in Rice ( Oryza sativa L.). Int J Mol Sci 2021; 22:ijms22147674. [PMID: 34299294 PMCID: PMC8304609 DOI: 10.3390/ijms22147674] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 07/10/2021] [Accepted: 07/15/2021] [Indexed: 01/21/2023] Open
Abstract
Nitrogen (N) is an essential nutrient for plant growth and development. The root system architecture is a highly regulated morphological system, which is sensitive to the availability of nutrients, such as N. Phenotypic characterization of roots from LY9348 (a rice variety with high nitrogen use efficiency (NUE)) treated with 0.725 mM NH4NO3 (1/4N) was remarkable, especially primary root (PR) elongation, which was the highest. A comprehensive analysis was performed for transcriptome and proteome profiling of LY9348 roots between 1/4N and 2.9 mM NH4NO3 (1N) treatments. The results indicated 3908 differential expression genes (DEGs; 2569 upregulated and 1339 downregulated) and 411 differential abundance proteins (DAPs; 192 upregulated and 219 downregulated). Among all DAPs in the proteome, glutamine synthetase (GS2), a chloroplastic ammonium assimilation protein, was the most upregulated protein identified. The unexpected concentration of GS2 from the shoot to the root in the 1/4N treatment indicated that the presence of an alternative pathway of N assimilation regulated by GS2 in LY9348 corresponded to the low N signal, which was supported by GS enzyme activity and glutamine/glutamate (Gln/Glu) contents analysis. In addition, N transporters (NRT2.1, NRT2.2, NRT2.3, NRT2.4, NAR2.1, AMT1.3, AMT1.2, and putative AMT3.3) and N assimilators (NR2, GS1;1, GS1;2, GS1;3, NADH-GOGAT2, and AS2) were significantly induced during the long-term N-deficiency response at the transcription level (14 days). Moreover, the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis demonstrated that phenylpropanoid biosynthesis and glutathione metabolism were significantly modulated by N deficiency. Notably, many transcription factors and plant hormones were found to participate in root morphological adaptation. In conclusion, our study provides valuable information to further understand the response of rice roots to N-deficiency stress.
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Affiliation(s)
- Ting Liang
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (T.L.); (Z.Y.); (L.F.); (M.Z.); (X.L.); (W.X.); (H.Y.); (R.Z.); (Z.H.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Zhengqing Yuan
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (T.L.); (Z.Y.); (L.F.); (M.Z.); (X.L.); (W.X.); (H.Y.); (R.Z.); (Z.H.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Lu Fu
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (T.L.); (Z.Y.); (L.F.); (M.Z.); (X.L.); (W.X.); (H.Y.); (R.Z.); (Z.H.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Menghan Zhu
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (T.L.); (Z.Y.); (L.F.); (M.Z.); (X.L.); (W.X.); (H.Y.); (R.Z.); (Z.H.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Xiaoyun Luo
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (T.L.); (Z.Y.); (L.F.); (M.Z.); (X.L.); (W.X.); (H.Y.); (R.Z.); (Z.H.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Wuwu Xu
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (T.L.); (Z.Y.); (L.F.); (M.Z.); (X.L.); (W.X.); (H.Y.); (R.Z.); (Z.H.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Huanran Yuan
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (T.L.); (Z.Y.); (L.F.); (M.Z.); (X.L.); (W.X.); (H.Y.); (R.Z.); (Z.H.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Renshan Zhu
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (T.L.); (Z.Y.); (L.F.); (M.Z.); (X.L.); (W.X.); (H.Y.); (R.Z.); (Z.H.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Zhongli Hu
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (T.L.); (Z.Y.); (L.F.); (M.Z.); (X.L.); (W.X.); (H.Y.); (R.Z.); (Z.H.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Xianting Wu
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (T.L.); (Z.Y.); (L.F.); (M.Z.); (X.L.); (W.X.); (H.Y.); (R.Z.); (Z.H.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
- Crop Research Institute, Sichuan Academy of Agricultural Science, Chengdu 610000, China
- Correspondence: ; Tel.: +86-181-8061-4938
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50
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Proofing Direct-Seeded Rice with Better Root Plasticity and Architecture. Int J Mol Sci 2021; 22:ijms22116058. [PMID: 34199720 PMCID: PMC8199995 DOI: 10.3390/ijms22116058] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 05/30/2021] [Accepted: 06/01/2021] [Indexed: 11/16/2022] Open
Abstract
The underground reserve (root) has been an uncharted research territory with its untapped genetic variation yet to be exploited. Identifying ideal traits and breeding new rice varieties with efficient root system architecture (RSA) has great potential to increase resource-use efficiency and grain yield, especially under direct-seeded rice, by adapting to aerobic soil conditions. In this review, we tried to mine the available research information on the direct-seeded rice (DSR) root system to highlight the requirements of different root traits such as root architecture, length, number, density, thickness, diameter, and angle that play a pivotal role in determining the uptake of nutrients and moisture at different stages of plant growth. RSA also faces several stresses, due to excess or deficiency of moisture and nutrients, low or high temperature, or saline conditions. To counteract these hindrances, adaptation in response to stress becomes essential. Candidate genes such as early root growth enhancer PSTOL1, surface rooting QTL qSOR1, deep rooting gene DRO1, and numerous transporters for their respective nutrients and stress-responsive factors have been identified and validated under different circumstances. Identifying the desired QTLs and transporters underlying these traits and then designing an ideal root architecture can help in developing a suitable DSR cultivar and aid in further advancement in this direction.
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