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Liu C, Gu W, Liu C, Shi X, Li B, Zhou Y. Comparative phenotypic and transcriptomic analysis reveals genotypic differences in nitrogen use efficiency in sorghum. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 215:109028. [PMID: 39146913 DOI: 10.1016/j.plaphy.2024.109028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 07/27/2024] [Accepted: 08/06/2024] [Indexed: 08/17/2024]
Abstract
Sorghum (Sorghumbicolor L.), a model for C4 grass and an emerging biofuel crop, is known for its robust tolerance to low input field. However, the focus on enhancing nitrogen use efficiency (NUE) in sorghum under low nitrogen (N) conditions has been limited. This study conducted hydroponic experiments and field trials with two sorghum inbred lines, contrasting in their N efficiency: the N-efficient (398B) and the N-inefficient (CS3541) inbred lines. The aim was to analyze the key factors influencing NUE by integrating phenotypic, physiological, and multi-omics approaches under N deficiency conditions. The field experiments revealed that 398B displayed superior NUE and yield performance compared to CS3541. In hydroponic experiments, the growth of 398B outperformed CS3541 following N deficiency, attributing to its higher photosynthetic and sustaining activity of N metabolism-related enzymes. Genomic and transcriptomic integration highlighted fewer genomic diversities and alterations in global gene expression in 398B, which were likely contributor to its high NUE. Additionally, co-expression network analysis suggested the involvement of key genes which impact N uptake efficiency (NUpE) and N utilization efficiency (NUtE) in both lines, such as an N transporter, Sobic.003G371000.v3.2leaf(NPF5.10) and a transcription factor, Sobic.002G202800.v3.2leaf(WRKY) in bolstering NUE under low-N stress. The findings collectively suggested that 398B achieved higher NUpE and NUtE, effectively coordinating photosynthesis and N metabolism to enhance NUE. The candidate genes regulating N uptake and utilization efficiencies could provide valuable insights for developing sorghum breeds with improved NUE, contributing to sustainable agricultural practices and bioenergy crop development.
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Affiliation(s)
- Chunjuan Liu
- College of Agronomy/Shenyang Agricultural University, Shenyang, Liaoning, 110866, PR China
| | - Wendong Gu
- College of Agronomy/Shenyang Agricultural University, Shenyang, Liaoning, 110866, PR China
| | - Chang Liu
- College of Agronomy/Shenyang Agricultural University, Shenyang, Liaoning, 110866, PR China
| | - Xiaolong Shi
- College of Agronomy/Shenyang Agricultural University, Shenyang, Liaoning, 110866, PR China
| | - Bang Li
- College of Agronomy/Shenyang Agricultural University, Shenyang, Liaoning, 110866, PR China
| | - Yufei Zhou
- College of Agronomy/Shenyang Agricultural University, Shenyang, Liaoning, 110866, PR China.
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Zhao H, Ge M, Zhang F, Du D, Zhao Z, Shen C, Hao Q, Xiao M, Shi X, Wang J, Fan M. Integrated morphological, physiological and transcriptomic analyses reveal the responses of Toona sinensis seedlings to low-nitrogen stress. Genomics 2024; 116:110899. [PMID: 39047875 DOI: 10.1016/j.ygeno.2024.110899] [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: 12/09/2023] [Revised: 07/03/2024] [Accepted: 07/20/2024] [Indexed: 07/27/2024]
Abstract
Nitrogen is one of the most essential elements for plant growth and development. In this study, the growth, physiology, and transcriptome of Toona sinensis (A. Juss) Roem seedlings were compared between low-nitrogen (LN) and normal-nitrogen (NN) conditions. These results indicate that LN stress adversely influences T. sinensis seedling growth. The activities of key enzymes related to nitrogen assimilation and phytohormone contents were altered by LN stress. A total of 2828 differentially expressed genes (DEGs) in roots and 1547 in leaves were identified between the LN and NN treatments. A differential enrichment analysis of Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways indicated that nitrogen and sugar metabolism, flavonoid biosynthesis, plant hormone signal transduction, and ABC transporters, were strongly affected by LN stress. In summary, this research provides information for further understanding the response of T. sinensis to LN stress.
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Affiliation(s)
- Hu Zhao
- Biology and Food Engineering College, Fuyang Normal University, Anhui 236037, People's Republic of China.
| | - Miaomiao Ge
- Biology and Food Engineering College, Fuyang Normal University, Anhui 236037, People's Republic of China
| | - Fengzhe Zhang
- Biology and Food Engineering College, Fuyang Normal University, Anhui 236037, People's Republic of China
| | - Didi Du
- Biology and Food Engineering College, Fuyang Normal University, Anhui 236037, People's Republic of China
| | - Zilu Zhao
- Biology and Food Engineering College, Fuyang Normal University, Anhui 236037, People's Republic of China
| | - Cheng Shen
- Biology and Food Engineering College, Fuyang Normal University, Anhui 236037, People's Republic of China
| | - Qingping Hao
- Biology and Food Engineering College, Fuyang Normal University, Anhui 236037, People's Republic of China
| | - Min Xiao
- Biology and Food Engineering College, Fuyang Normal University, Anhui 236037, People's Republic of China
| | - Xiaopu Shi
- Biology and Food Engineering College, Fuyang Normal University, Anhui 236037, People's Republic of China.
| | - Juan Wang
- Biology and Food Engineering College, Fuyang Normal University, Anhui 236037, People's Republic of China
| | - Mingqin Fan
- Biology and Food Engineering College, Fuyang Normal University, Anhui 236037, People's Republic of China
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Gu J, Guan Z, Jiao Y, Liu K, Hong D. The story of a decade: Genomics, functional genomics, and molecular breeding in Brassica napus. PLANT COMMUNICATIONS 2024; 5:100884. [PMID: 38494786 PMCID: PMC11009362 DOI: 10.1016/j.xplc.2024.100884] [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: 11/06/2023] [Revised: 03/01/2024] [Accepted: 03/14/2024] [Indexed: 03/19/2024]
Abstract
Rapeseed (Brassica napus L.) is one of the major global sources of edible vegetable oil and is also used as a feed and pioneer crop and for sightseeing and industrial purposes. Improvements in genome sequencing and molecular marker technology have fueled a boom in functional genomic studies of major agronomic characters such as yield, quality, flowering time, and stress resistance. Moreover, introgression and pyramiding of key functional genes have greatly accelerated the genetic improvement of important traits. Here we summarize recent progress in rapeseed genomics and genetics, and we discuss effective molecular breeding strategies by exploring these findings in rapeseed. These insights will extend our understanding of the molecular mechanisms and regulatory networks underlying agronomic traits and facilitate the breeding process, ultimately contributing to more sustainable agriculture throughout the world.
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Affiliation(s)
- Jianwei Gu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, Hubei, China; College of Life Science and Technology, Hubei Engineering University, Xiaogan 432100 Hubei, China
| | - Zhilin Guan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, Hubei, China; Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074 Hubei, China
| | - Yushun Jiao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Kede Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
| | - Dengfeng Hong
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, Hubei, China; Yazhouwan National Laboratory, Sanya 572024 Hainan, China.
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Nan Y, Xie Y, He H, Wu H, Gao L, Atif A, Zhang Y, Tian H, Hui J, Gao Y. Integrated BSA-seq and RNA-seq analysis to identify candidate genes associated with nitrogen utilization efficiency (NUtE) in rapeseed (Brassica napus L.). Int J Biol Macromol 2024; 254:127771. [PMID: 38287600 DOI: 10.1016/j.ijbiomac.2023.127771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 10/26/2023] [Accepted: 10/27/2023] [Indexed: 01/31/2024]
Abstract
Rapeseed (Brassica napus L.) is one of the important oil crops, with a high demand for nitrogen (N). It is essential to explore the potential of rapeseed to improve nitrogen utilization efficiency (NUtE). Rapeseed is an allotetraploid crop with a relatively large and complex genome, and there are few studies on the mapping of genes related to NUtE regulation. In this study, we used the combination of bulk segregant analysis sequencing (BSA-Seq) and RNA sequencing (RNA-Seq) to analyze the N-efficient genotype 'Zheyou 18' and N-inefficient genotype 'Sollux', to identify the genetic regulatory mechanisms. Several candidate genes were screened, such as the high-affinity nitrate transporter gene NRT2.1 (BnaC08g43370D) and the abscisic acid (ABA) signal transduction-related genes (BnaC02g14540D, BnaA03g20760D, and BnaA05g01330D). BnaA05g01330D was annotated as ABA-INDUCIBLE bHLH-TYPE TRANSCRIPTION FACTOR (AIB/bHLH17), which was highly expressed in the root. The results showed that the primary root length of the ataib mutant was significantly longer than that of the wild type under low N conditions. Overexpression of BnaA5.AIB could reduce the NUtE under low N levels in Arabidopsis (Arabidopsis thaliana). Candidate genes identified in this study may be involved in the regulation of NUtE in rapeseed, and new functions of AIB in orchestrating N uptake and utilization have been revealed. It is indicated that BnaA5.AIB may be the key factor that links ABA to N signaling and a negative regulator of NUtE. It will provide a theoretical basis and application prospect for resource conservation, environmental protection, and sustainable agricultural development.
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Affiliation(s)
- Yunyou Nan
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, China
| | - Yuyu Xie
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, China
| | - Huiying He
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, China
| | - Han Wu
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, China
| | - Lixing Gao
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, China
| | - Ayub Atif
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, China
| | - Yanfeng Zhang
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, Shaanxi, China
| | - Hui Tian
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, China.
| | - Jing Hui
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, China.
| | - Yajun Gao
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi, China.
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Chen E, Qin L, Li F, Yang Y, Liu Z, Wang R, Yu X, Niu J, Zhang H, Wang H, Liu B, Guan Y. Physiological and Transcriptomic Analysis Provides Insights into Low Nitrogen Stress in Foxtail Millet ( Setaria italica L.). Int J Mol Sci 2023; 24:16321. [PMID: 38003509 PMCID: PMC10671652 DOI: 10.3390/ijms242216321] [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: 10/17/2023] [Revised: 11/07/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023] Open
Abstract
Foxtail millet (Setaria italica (L.) P. Beauv) is an important food and forage crop that is well adapted to nutrient-poor soils. However, our understanding of how different LN-tolerant foxtail millet varieties adapt to long-term low nitrogen (LN) stress at the physiological and molecular levels remains limited. In this study, two foxtail millet varieties with contrasting LN tolerance properties were investigated through analyses of physiological parameters and transcriptomics. The physiological results indicate that JG20 (high tolerance to LN) exhibited superior biomass accumulation both in its shoots and roots, and higher nitrogen content, soluble sugar concentration, soluble protein concentration, zeatin concentration in shoot, and lower soluble sugar and soluble protein concentration in its roots compared to JG22 (sensitive to LN) under LN, this indicated that the LN-tolerant foxtail millet variety can allocate more functional substance to its shoots to sustain aboveground growth and maintain high root activity by utilizing low soluble sugar and protein under LN conditions. In the transcriptomics analysis, JG20 exhibited a greater number of differentially expressed genes (DEGs) compared to JG22 in both its shoots and roots in response to LN stress. These LN-responsive genes were enriched in glycolysis metabolism, photosynthesis, hormone metabolism, and nitrogen metabolism. Furthermore, in the shoots, the glutamine synthetase gene SiGS5, chlorophyll apoprotein of photosystem II gene SiPsbQ, ATP synthase subunit gene Sib, zeatin synthesis genes SiAHP1, and aldose 1-epimerase gene SiAEP, and, in the roots, the high-affinity nitrate transporter genes SiNRT2.3, SiNRT2.4, glutamate synthase gene SiGOGAT2, fructose-bisphosphate aldolase gene SiFBA5, were important genes involved in the LN tolerance of the foxtail millet variety. Hence, our study implies that the identified genes and metabolic pathways contribute valuable insights into the mechanisms underlying LN tolerance in foxtail millet.
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Affiliation(s)
- Erying Chen
- Featured Crops Engineering Laboratory of Shandong Province, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (E.C.); (L.Q.); (F.L.); (Y.Y.); (Z.L.); (R.W.); (H.Z.); (H.W.); (B.L.)
| | - Ling Qin
- Featured Crops Engineering Laboratory of Shandong Province, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (E.C.); (L.Q.); (F.L.); (Y.Y.); (Z.L.); (R.W.); (H.Z.); (H.W.); (B.L.)
| | - Feifei Li
- Featured Crops Engineering Laboratory of Shandong Province, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (E.C.); (L.Q.); (F.L.); (Y.Y.); (Z.L.); (R.W.); (H.Z.); (H.W.); (B.L.)
| | - Yanbing Yang
- Featured Crops Engineering Laboratory of Shandong Province, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (E.C.); (L.Q.); (F.L.); (Y.Y.); (Z.L.); (R.W.); (H.Z.); (H.W.); (B.L.)
| | - Zhenyu Liu
- Featured Crops Engineering Laboratory of Shandong Province, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (E.C.); (L.Q.); (F.L.); (Y.Y.); (Z.L.); (R.W.); (H.Z.); (H.W.); (B.L.)
| | - Runfeng Wang
- Featured Crops Engineering Laboratory of Shandong Province, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (E.C.); (L.Q.); (F.L.); (Y.Y.); (Z.L.); (R.W.); (H.Z.); (H.W.); (B.L.)
| | - Xiao Yu
- College of Life Science, Shandong Normal University, Jinan 250014, China; (X.Y.); (J.N.)
| | - Jiahong Niu
- College of Life Science, Shandong Normal University, Jinan 250014, China; (X.Y.); (J.N.)
| | - Huawen Zhang
- Featured Crops Engineering Laboratory of Shandong Province, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (E.C.); (L.Q.); (F.L.); (Y.Y.); (Z.L.); (R.W.); (H.Z.); (H.W.); (B.L.)
| | - Hailian Wang
- Featured Crops Engineering Laboratory of Shandong Province, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (E.C.); (L.Q.); (F.L.); (Y.Y.); (Z.L.); (R.W.); (H.Z.); (H.W.); (B.L.)
| | - Bin Liu
- Featured Crops Engineering Laboratory of Shandong Province, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (E.C.); (L.Q.); (F.L.); (Y.Y.); (Z.L.); (R.W.); (H.Z.); (H.W.); (B.L.)
| | - Yanan Guan
- Featured Crops Engineering Laboratory of Shandong Province, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (E.C.); (L.Q.); (F.L.); (Y.Y.); (Z.L.); (R.W.); (H.Z.); (H.W.); (B.L.)
- College of Life Science, Shandong Normal University, Jinan 250014, China; (X.Y.); (J.N.)
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Banerjee S, Mukherjee A, Kundu A. The current scenario and future perspectives of transgenic oilseed mustard by CRISPR-Cas9. Mol Biol Rep 2023; 50:7705-7728. [PMID: 37432544 DOI: 10.1007/s11033-023-08660-6] [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: 09/02/2022] [Accepted: 06/30/2023] [Indexed: 07/12/2023]
Abstract
PURPOSE Production of a designer crop having added attributes is the primary goal of all plant biotechnologists. Specifically, development of a crop with a simple biotechnological approach and at a rapid pace is most desirable. Genetic engineering enables us to displace genes among species. The newly incorporated foreign gene(s) in the host genome can create a new trait(s) by regulating the genotypes and/or phenotypes. The advent of the CRISPR-Cas9 tools has enabled the modification of a plant genome easily by introducing mutation or replacing genomic fragment. Oilseed mustard varieties (e.g., Brassica juncea, Brassica nigra, Brassica napus, and Brassica carinata) are one such plants, which have been transformed with different genes isolated from the wide range of species. Current reports proved that the yield and value of oilseed mustard has been tremendously improved by the introduction of stably inherited new traits such as insect and herbicide resistance. However, the genetic transformation of oilseed mustard remains incompetent due to lack of potential plant transformation systems. To solve numerous complications involved in genetically modified oilseed mustard crop varieties regeneration procedures, scientific research is being conducted to rectify the unwanted complications. Thus, this study provides a broader overview of the present status of new traits introduced in each mentioned varieties of oilseed mustard plant by different genetical engineering tools, especially CRISPR-Cas9, which will be useful to improve the transformation system of oilseed mustard crop plants. METHODS This review presents recent improvements made in oilseed mustard genetic engineering methodologies by using CRISPR-Cas9 tools, present status of new traits introduced in oilseed mustard plant varieties. RESULTS The review highlighted that the transgenic oilseed mustard production is a challenging process and the transgenic varieties of oilseed mustard provide a powerful tool for enhanced mustard yield. Over expression studies and silencing of desired genes provide functional importance of genes involved in mustard growth and development under different biotic and abiotic stress conditions. Thus, it can be expected that in near future CRISPR can contribute enormously in improving the mustard plant's architecture and develop stress resilient oilseed mustard plant species.
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Affiliation(s)
- Sangeeta Banerjee
- Department of Microbiology, Techno India University, EM-4, Sector-V, Saltlake City, Kolkata, West Bengal, 700091, India
| | - Ananya Mukherjee
- Division of Plant Biology, Bose Institute, EN 80, Sector V, Bidhan Nagar, Kolkata, WB, 700091, India
| | - Atreyee Kundu
- Department of Microbiology, Techno India University, EM-4, Sector-V, Saltlake City, Kolkata, West Bengal, 700091, India.
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Fiaz M, Ahmed I, Hassan SMU, Niazi AK, Khokhar MF, Farooq MA, Arshad M. Antibiotics induced changes in nitrogen metabolism and antioxidative enzymes in mung bean (Vigna radiata). THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 873:162449. [PMID: 36841411 DOI: 10.1016/j.scitotenv.2023.162449] [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: 11/22/2022] [Revised: 02/18/2023] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
Excessive use and release of antibiotics into the soil environment in the developing world have resulted in altered soil processes affecting terrestrial organisms and posing a serious threat to crop growth and productivity. The present study investigated the influence of exogenously applied oxytetracycline (OXY) and levofloxacin (LEV) on plant physiological responses, key enzymes involved in nitrogen metabolism (e.g., nitrate reductase, glutamine synthetase), nitrogen contents and oxidative stress response of mung bean (Vigna radiata). Plants were irrigated weekly with antibiotics containing water for exposing the plants to different concentrations i.e., 1, 10, 20, 50, and 100 mg L-1. Results showed a significant decrease in nitrate reductase activity in both antibiotic treatments and their mixtures and increased antioxidant enzymatic activities in plants. At lower concentrations of antibiotics (≤20 mg L-1), 53.9 % to 78.4 % increase in nitrogen content was observed in levofloxacin and mixtures compared to the control, resulting in an increase in the overall plant biomass. Higher antibiotic (≥50 mg L-1) concentration showed 58 % decrease in plant biomass content and an overall decrease in plant nitrogen content upon exposure to the mixtures. This was further complemented by 22 % to 42 % increase in glutamine synthetase activity observed in the plants treated with levofloxacin and mixtures. The application of low doses of antibiotics throughout the experiments resulted in lower toxicity symptoms in the plants. However, significantly higher malondialdehyde (MDA) concentrations at higher doses (20 mg L-1 and above) than the control showed that plants' tolerance against oxidative stress was conceded with increasing antibiotic concentrations. The toxicity trend was: levofloxacin > mixture > oxytetracycline.
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Affiliation(s)
- Marium Fiaz
- Institute of Environmental Sciences and Engineering, School of Civil and Environmental Engineering, National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Iftikhar Ahmed
- National Culture Collection of Pakistan (NCCP), Land Resources Research Institute (LRRI), National Agriculture Research Center (NARC), Islamabad, Pakistan
| | - Sumara Masood Ul Hassan
- School of Social Sciences and Humanities, National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Adnan Khan Niazi
- Centre for Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan
| | - Muhammad Fahim Khokhar
- Institute of Environmental Sciences and Engineering, School of Civil and Environmental Engineering, National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Muhammad Ansar Farooq
- Institute of Environmental Sciences and Engineering, School of Civil and Environmental Engineering, National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Muhammad Arshad
- Institute of Environmental Sciences and Engineering, School of Civil and Environmental Engineering, National University of Sciences and Technology (NUST), Islamabad, Pakistan.
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Li P, Du R, Li Z, Chen Z, Li J, Du H. An integrated nitrogen utilization gene network and transcriptome analysis reveal candidate genes in response to nitrogen deficiency in Brassica napus. FRONTIERS IN PLANT SCIENCE 2023; 14:1187552. [PMID: 37229128 PMCID: PMC10203523 DOI: 10.3389/fpls.2023.1187552] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 04/21/2023] [Indexed: 05/27/2023]
Abstract
Nitrogen (N) is an essential factor for crop yield. Here, we characterized 605 genes from 25 gene families that form the complex gene networks of N utilization pathway in Brassica napus. We found unequal gene distribution between the An- and Cn-sub-genomes, and that genes derived from Brassica rapa were more retained. Transcriptome analysis indicated that N utilization pathway gene activity shifted in a spatio-temporal manner in B. napus. A low N (LN) stress RNA-seq of B. napus seedling leaves and roots was generated, which proved that most N utilization related genes were sensitive to LN stress, thereby forming co-expression network modules. Nine candidate genes in N utilization pathway were confirmed to be significantly induced under N deficiency conditions in B. napus roots, indicating their potential roles in LN stress response process. Analyses of 22 representative species confirmed that the N utilization gene networks were widely present in plants ranging from Chlorophyta to angiosperms with a rapid expansion trend. Consistent with B. napus, the genes in this pathway commonly showed a wide and conserved expression profile in response to N stress in other plants. The network, genes, and gene-regulatory modules identified here represent resources that may enhance the N utilization efficiency or the LN tolerance of B. napus.
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Affiliation(s)
- Pengfeng Li
- College of Agronomy and Biotechnology, Chongqing Engineering Research Center for Rapeseed, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Runjie Du
- College of Agronomy and Biotechnology, Chongqing Engineering Research Center for Rapeseed, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Zhaopeng Li
- College of Agronomy and Biotechnology, Chongqing Engineering Research Center for Rapeseed, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Zhuo Chen
- College of Agronomy and Biotechnology, Chongqing Engineering Research Center for Rapeseed, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Jiana Li
- College of Agronomy and Biotechnology, Chongqing Engineering Research Center for Rapeseed, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Hai Du
- College of Agronomy and Biotechnology, Chongqing Engineering Research Center for Rapeseed, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
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Zhan N, Xu K, Ji G, Yan G, Chen B, Wu X, Cai G. Research Progress in High-Efficiency Utilization of Nitrogen in Rapeseed. Int J Mol Sci 2023; 24:ijms24097752. [PMID: 37175459 PMCID: PMC10177885 DOI: 10.3390/ijms24097752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/17/2023] [Accepted: 04/22/2023] [Indexed: 05/15/2023] Open
Abstract
Nitrogen (N) is one of the most important mineral elements for plant growth and development and a key factor for improving crop yield. Rapeseed, Brassica napus, is the largest oil crop in China, producing more than 50% of the domestic vegetable oil. However, high N fertilizer input with low utilization efficiency not only increases the production cost but also causes serious environmental pollution. Therefore, the breeding of rapeseed with high N efficiency is of great strategic significance to ensure the security of grain and oil and the sustainable development of the rapeseed industry. In order to provide reference for genetic improvement of rapeseed N-efficient utilization, in this article, we mainly reviewed the recent research progress of rapeseed N efficiency, including rapeseed N efficiency evaluation, N-efficient germplasm screening, and N-efficient physiological and molecular genetic mechanisms.
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Affiliation(s)
- Na Zhan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Kun Xu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Gaoxiang Ji
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Guixin Yan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Biyun Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Xiaoming Wu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Guangqin Cai
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
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Bashir SS, Siddiqi TO, Kumar D, Ahmad A. Physio-biochemical, agronomical, and gene expression analysis reveals different responsive approach to low nitrogen in contrasting rice cultivars for nitrogen use efficiency. Mol Biol Rep 2023; 50:1575-1593. [PMID: 36520360 DOI: 10.1007/s11033-022-08160-z] [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: 08/19/2022] [Accepted: 11/24/2022] [Indexed: 12/23/2022]
Abstract
BACKGROUND Nitrogen (N) is an essential macronutrient for plant growth and development as it is an essential constituent of biomolecules. Its availability directly impacts crop yield. Increased N application in crop fields has caused environmental and health problems, and decreasing nitrogen inputs are in demand to maintain crop production sustainability. Understanding the molecular mechanism of N utilization could play a crucial role in improving the nitrogen use efficiency (NUE) of crop plants. METHODS AND RESULTS In the present study, the effect of low N supply on plant growth, physio-biochemical, chlorophyll fluorescence attributes, yield components, and gene expression analysis were measured at six developmental stages in rice cultivars. Two rice cultivars were grown with a supply of optimium (120 kg ha-1) and low N (60 kg ha-1). Cultivar Vikramarya excelled Aditya at low N supply, and exhibits enhanced plant growth, physiological efficiency, agronomic efficiency, and improved NUE due to higher N uptake and utilization at low N treatment. Moreover, plant biomass, leaf area, and photosynthetic rate were significantly higher in cv. Vikramarya than cv. Aditya at different growth stages, under low N treatment. In addition, enzymatic activities in cultivar Vikramarya were higher than cultivar Aditya under low nitrogen, indicating its greater potential for N metabolism. Gene expression analysis was carried out for the most important nitrogen assimilatory enzymes, such as nitrate reductase (NR), nitrite reductase (NiR), glutamine synthetase (GS), and glutamate synthase (GOGAT). Expression levels of these genes at different growth stages were significantly higher in cv. Vikramarya compared to cv. Aditya at low N supply. Our findings suggest that improving NUE needs specific revision in N metabolism and physiological assimilation. CONCLUSION Overall differences in plant growth, physiological efficiency, biochemical activities, and expression levels of N metabolism genes in N-efficient and N-inefficient rice cultivars need a specific adaptation to N metabolism. Regulatory genes may separately or in conjunction, enhance the NUE. These results provide a platform for selecting crop cultivars for nitrogen utilization efficiency at low N treatment.
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Affiliation(s)
- Sheikh Shanawaz Bashir
- Department of Botany, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, India
| | - Tariq Omar Siddiqi
- Department of Botany, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, India
| | - Dinesh Kumar
- Division of Agronomy, Indian Agricultural Research Institute, New Delhi, India
| | - Altaf Ahmad
- Department of Botany, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, India.
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11
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Hodin J, Lind C, Marmagne A, Espagne C, Bianchi MW, De Angeli A, Abou-Choucha F, Bourge M, Chardon F, Thomine S, Filleur S. Proton exchange by the vacuolar nitrate transporter CLCa is required for plant growth and nitrogen use efficiency. THE PLANT CELL 2023; 35:318-335. [PMID: 36409008 PMCID: PMC9806559 DOI: 10.1093/plcell/koac325] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 11/03/2022] [Indexed: 06/16/2023]
Abstract
Nitrate is a major nutrient and osmoticum for plants. To deal with fluctuating nitrate availability in soils, plants store this nutrient in their vacuoles. Chloride channel a (CLCa), a 2NO3-/1H+ exchanger localized to the vacuole in Arabidopsis (Arabidopsis thaliana), ensures this storage process. CLCa belongs to the CLC family, which includes anion/proton exchangers and anion channels. A mutation in a glutamate residue conserved across CLC exchangers is likely responsible for the conversion of exchangers to channels. Here, we show that CLCa with a mutation in glutamate 203 (E203) behaves as an anion channel in its native membrane. We introduced the CLCaE203A point mutation to investigate its physiological importance into the Arabidopsis clca knockout mutant. These CLCaE203A mutants displayed a growth deficit linked to the disruption of water homeostasis. Additionally, CLCaE203A expression failed to complement the defect in nitrate accumulation of clca and favored higher N-assimilation at the vegetative stage. Further analyses at the post-flowering stages indicated that CLCaE203A expression results in an increase in N uptake allocation to seeds, leading to a higher nitrogen use efficiency compared to the wild-type. Altogether, these results point to the critical function of the CLCa exchanger on the vacuole for plant metabolism and development.
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Affiliation(s)
- Julie Hodin
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France
- UFR Sciences du Vivant, Université Paris Cité, F-75205 Paris Cedex 13, France
| | - Christof Lind
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France
| | - Anne Marmagne
- AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Université Paris-Saclay, INRAE, 78000 Versailles, France
| | - Christelle Espagne
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France
| | - Michele Wolfe Bianchi
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France
- Université Paris-Est-Créteil-Val-de-Marne, 94010 Creteil Cedex, France
| | - Alexis De Angeli
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France
| | - Fadi Abou-Choucha
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France
| | - Mickaël Bourge
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France
| | - Fabien Chardon
- AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Université Paris-Saclay, INRAE, 78000 Versailles, France
| | - Sebastien Thomine
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France
| | - Sophie Filleur
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France
- UFR Sciences du Vivant, Université Paris Cité, F-75205 Paris Cedex 13, France
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12
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Hua YP, Wu PJ, Zhang TY, Song HL, Zhang YF, Chen JF, Yue CP, Huang JY, Sun T, Zhou T. Genome-Scale Investigation of GARP Family Genes Reveals Their Pivotal Roles in Nutrient Stress Resistance in Allotetraploid Rapeseed. Int J Mol Sci 2022; 23:ijms232214484. [PMID: 36430962 PMCID: PMC9698747 DOI: 10.3390/ijms232214484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 11/14/2022] [Accepted: 11/18/2022] [Indexed: 11/23/2022] Open
Abstract
The GARP genes are plant-specific transcription factors (TFs) and play key roles in regulating plant development and abiotic stress resistance. However, few systematic analyses of GARPs have been reported in allotetraploid rapeseed (Brassica napus L.) yet. In the present study, a total of 146 BnaGARP members were identified from the rapeseed genome based on the sequence signature. The BnaGARP TFs were divided into five subfamilies: ARR, GLK, NIGT1/HRS1/HHO, KAN, and PHL subfamilies, and the members within the same subfamilies shared similar exon-intron structures and conserved motif configuration. Analyses of the Ka/Ks ratios indicated that the GARP family principally underwent purifying selection. Several cis-acting regulatory elements, essential for plant growth and diverse biotic and abiotic stresses, were identified in the promoter regions of BnaGARPs. Further, 29 putative miRNAs were identified to be targeting BnaGARPs. Differential expression of BnaGARPs under low nitrate, ammonium toxicity, limited phosphate, deficient boron, salt stress, and cadmium toxicity conditions indicated their potential involvement in diverse nutrient stress responses. Notably, BnaA9.HHO1 and BnaA1.HHO5 were simultaneously transcriptionally responsive to these nutrient stresses in both hoots and roots, which indicated that BnaA9.HHO1 and BnaA1.HHO5 might play a core role in regulating rapeseed resistance to nutrient stresses. Therefore, this study would enrich our understanding of molecular characteristics of the rapeseed GARPs and will provide valuable candidate genes for further in-depth study of the GARP-mediated nutrient stress resistance in rapeseed.
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Affiliation(s)
- Ying-Peng Hua
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Peng-Jia Wu
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Tian-Yu Zhang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Hai-Li Song
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Yi-Fan Zhang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Jun-Fan Chen
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Cai-Peng Yue
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Jin-Yong Huang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Tao Sun
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
- Correspondence: (T.S.); (T.Z.); Tel.: +86-187-0271-0749 (T.Z.)
| | - Ting Zhou
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
- Correspondence: (T.S.); (T.Z.); Tel.: +86-187-0271-0749 (T.Z.)
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13
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Guo H, He X, Zhang H, Tan R, Yang J, Xu F, Wang S, Yang C, Ding G. Physiological Responses of Cigar Tobacco Crop to Nitrogen Deficiency and Genome-Wide Characterization of the NtNPF Family Genes. PLANTS (BASEL, SWITZERLAND) 2022; 11:3064. [PMID: 36432793 PMCID: PMC9697317 DOI: 10.3390/plants11223064] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 11/02/2022] [Accepted: 11/10/2022] [Indexed: 06/16/2023]
Abstract
Tobacco prefers nitrate as a nitrogen (N) source. However, little is known about the molecular components responsible for nitrate uptake and the physiological responses of cigar tobacco to N deficiency. In this study, a total of 117 nitrate transporter 1 (NRT1) and peptide transporter (PTR) family (NPF) genes were comprehensively identified and systematically characterized in the whole tobacco genome. The NtNPF members showed significant genetic diversity within and across subfamilies but showed conservation between subfamilies. The NtNPF genes are dispersed unevenly across the chromosomes. The phylogenetic analysis revealed that eight subfamilies of NtNPF genes are tightly grouped with their orthologues in Arabidopsis. The promoter regions of the NtNPF genes had extensive cis-regulatory elements. Twelve core NtNPF genes, which were strongly induced by N limitation, were identified based on the RNA-seq data. Furthermore, N deprivation severely impaired plant growth of two cigar tobaccos, and CX26 may be more sensitive to N deficiency than CX14. Moreover, 12 hub genes respond differently to N deficiency between the two cultivars, indicating the vital roles in regulating N uptake and transport in cigar tobacco. The findings here contribute towards a better knowledge of the NtNPF genes and lay the foundation for further functional analysis of cigar tobacco.
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Affiliation(s)
- Hao Guo
- Microelement Research Center, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Xuyou He
- Microelement Research Center, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Hao Zhang
- Microelement Research Center, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Ronglei Tan
- Microelement Research Center, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinpeng Yang
- Tobacco Research Institute of Hubei Province, Wuhan 430030, China
| | - Fangsen Xu
- Microelement Research Center, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Sheliang Wang
- Microelement Research Center, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Chunlei Yang
- Tobacco Research Institute of Hubei Province, Wuhan 430030, China
| | - Guangda Ding
- Microelement Research Center, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
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14
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Hu Y, Guy RD, Soolanayakanahally RY. Nitrogen isotope discrimination in open-pollinated and hybrid canola suggests indirect selection for enhanced ammonium utilization. FRONTIERS IN PLANT SCIENCE 2022; 13:1024080. [PMID: 36438099 PMCID: PMC9691982 DOI: 10.3389/fpls.2022.1024080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 10/25/2022] [Indexed: 06/16/2023]
Abstract
Nitrogen isotope discrimination (Δ15N) may have utility as an indicator of nitrogen use in plants. A simple Δ15N-based isotope mass balance (IMB) model has been proposed to provide estimates of efflux/influx (E/I) ratios across root plasma membranes, the proportion of inorganic nitrogen assimilation in roots (P root) and translocation of inorganic nitrogen to shoots (Ti/Tt) under steady-state conditions. We used the IMB model to investigate whether direct selection for yield in canola (Brassica napus L.) has resulted in indirect selection in traits related to nitrogen use. We selected 23 canola lines developed from 1942 to 2017, including open-pollinated (OP) lines developed prior to 2005 as well as more recent commercial hybrids (CH), and in three separate experiments grew them under hydroponic conditions in a greenhouse with either 0.5 mM ammonium, 0.5 mM nitrate, or 5 mM nitrate. Across all lines, E/I, Proot and Ti/Tt averaged 0.09±0.03, 0.82±0.05 and 0.23±0.06 in the low nitrate experiment, and 0.31±0.06, 0.71±0.07 and 0.42±0.12 in the high nitrate experiment, respectively. In contrast, in the ammonium experiment average E/I was 0.40±0.05 while Ti/Tt averaged 0.07±0.04 and Proot averaged 0.97±0.02. Although there were few consistent differences between OP and CH under nitrate nutrition, commercial hybrids were collectively better able to utilize ammonium as their sole nitrogen source, demonstrating significantly greater overall biomass and a lower Proot and a higher Ti/Tt, suggesting a somewhat greater flux of ammonium to the shoot. Average root and whole-plant Δ15N were also slightly higher in CH lines, suggesting a small increase in E/I. An increased ability to tolerate and/or utilize ammonium in modern canola hybrids may have arisen under intensive mono-cropping.
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Affiliation(s)
- Yi Hu
- Key Laboratory of Mountain Surface Processes and Ecological Regulation, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu, China
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, BC, Canada
| | - Robert D. Guy
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, BC, Canada
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15
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Tantray AY, Hazzazi Y, Ahmad A. Physiological, Agronomical, and Proteomic Studies Reveal Crucial Players in Rice Nitrogen Use Efficiency under Low Nitrogen Supply. Int J Mol Sci 2022; 23:ijms23126410. [PMID: 35742855 PMCID: PMC9224494 DOI: 10.3390/ijms23126410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 06/03/2022] [Accepted: 06/06/2022] [Indexed: 11/26/2022] Open
Abstract
Excessive use of nitrogenous fertilizers to enhance rice productivity has become a significant source of nitrogen (N) pollution and reduced sustainable agriculture. However, little information about the physiology of different growth stages, agronomic traits, and associated genetic bases of N use efficiency (NUE) are available at low-N supply. Two rice (Oryza sativa L.) cultivars were grown with optimum N (120 kg ha−1) and low N (60 kg ha−1) supply. Six growth stages were analyzed to measure the growth and physiological traits, as well as the differential proteomic profiles, of the rice cultivars. Cultivar Panvel outclassed Nagina 22 at low-N supply and exhibited improved growth and physiology at most of the growth stages and agronomic efficiency due to higher N uptake and utilization at low-N supply. On average, photosynthetic rate, chlorophyll content, plant biomass, leaf N content, and grain yield were decreased in cultivar Nagina 22 than Panvel was 8%, 11%, 21%, 19%, and 22%, respectively, under low-N supply. Furthermore, proteome analyses revealed that many proteins were upregulated and downregulated at the different growth stages under low-N supply. These proteins are associated with N and carbon metabolism and other physiological processes. This supports the genotypic differences in photosynthesis, N assimilation, energy stabilization, and rice-protein yield. Our study suggests that enhancing NUE at low-N supply demands distinct modifications in N metabolism and physiological assimilation. The NUE may be regulated by key identified differentially expressed proteins. These proteins might be the targets for improving crop NUE at low-N supply.
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Affiliation(s)
- Aadil Yousuf Tantray
- Department of Botany, Aligarh Muslim University, Aligarh 202002, Uttar Pradesh, India;
| | - Yehia Hazzazi
- School of Biological Sciences, University of Aberdeen, Aberdeen AB24 3UU, UK;
- Biology Department, Faculty of Sciences, Jazan University, Jazan 45142, Saudi Arabia
| | - Altaf Ahmad
- Department of Botany, Aligarh Muslim University, Aligarh 202002, Uttar Pradesh, India;
- Correspondence:
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16
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Cao J, Zheng X, Xie D, Zhou H, Shao S, Zhou J. Autophagic pathway contributes to low-nitrogen tolerance by optimizing nitrogen uptake and utilization in tomato. HORTICULTURE RESEARCH 2022; 9:uhac068. [PMID: 35669705 PMCID: PMC9164271 DOI: 10.1093/hr/uhac068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 03/09/2022] [Indexed: 06/15/2023]
Abstract
Autophagy is a primary process involved in the degradation and reuse of redundant or damaged cytoplasmic components in eukaryotes. Autophagy has been demonstrated to facilitate nutrient recycling and remobilization by delivering intracellular materials to the vacuole for degradation in plants under nutrient starvation. However, the role of autophagy in nitrogen (N) uptake and utilization remains unknown. Here, we report that the ATG6-dependent autophagic pathway regulates N utilization in tomato (Solanum lycopersicum) under low-nitrogen (LN) conditions. Autophagy-disrupted mutants exhibited weakened biomass production and N accumulation compared with wild-type (WT), while ATG6 overexpression promoted autophagy and biomass production under LN stress. The N content in atg6 mutants decreased while that in ATG6-overexpressing lines increased due to the control of N transporter gene expression in roots under LN conditions. Furthermore, ATG6-dependent autophagy enhanced N assimilation efficiency and protein production in leaves. Nitrate reductase and nitrite reductase activities and expression were compromised in atg6 mutants but were enhanced in ATG6-overexpressing plants under LN stress. Moreover, ATG6-dependent autophagy increased plant carbon fixation and photosynthetic capacity. The quantum yield of photosystem II, photosynthetic N use efficiency and photosynthetic protein accumulation were compromised in atg6 mutants but were restored in ATG6-overexpressing plants. A WT scion grafted onto atg6 mutant rootstock and an atg6 scion grafted onto WT rootstock both exhibited inhibited LN-induced autophagy and N uptake and utilization. Thus, ATG6-dependent autophagy regulates not only N uptake and utilization as well as carbon assimilation but also nutrient recycling and remobilization in tomato plants experiencing LN stress.
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Affiliation(s)
- Jiajian Cao
- College of Horticulture, Hunan Agricultural University, Nonda Road 1, Changsha, 410128, China
- Department of Horticulture/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Yuhangtang Road 866, Hangzhou, 310058, China
| | - Xuelian Zheng
- Department of Horticulture/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Yuhangtang Road 866, Hangzhou, 310058, China
| | - Dongling Xie
- Department of Horticulture/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Yuhangtang Road 866, Hangzhou, 310058, China
| | - Hui Zhou
- Department of Horticulture/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Yuhangtang Road 866, Hangzhou, 310058, China
| | - Shujun Shao
- Department of Horticulture/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Yuhangtang Road 866, Hangzhou, 310058, China
- Key Laboratory of Horticultural Plants Growth, Development and Quality Improvement, Agricultural Ministry of China, Yuhangtang Road 866, Hangzhou, 310058, China
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Zoghbi-Rodríguez NM, Gamboa-Tuz SD, Pereira-Santana A, Rodríguez-Zapata LC, Sánchez-Teyer LF, Echevarría-Machado I. Phylogenomic and Microsynteny Analysis Provides Evidence of Genome Arrangements of High-Affinity Nitrate Transporter Gene Families of Plants. Int J Mol Sci 2021; 22:13036. [PMID: 34884876 PMCID: PMC8658032 DOI: 10.3390/ijms222313036] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/12/2021] [Accepted: 11/17/2021] [Indexed: 12/29/2022] Open
Abstract
Nitrate transporter 2 (NRT2) and NRT3 or nitrate-assimilation-related 2 (NAR2) proteins families form a two-component, high-affinity nitrate transport system, which is essential for the acquisition of nitrate from soils with low N availability. An extensive phylogenomic analysis across land plants for these families has not been performed. In this study, we performed a microsynteny and orthology analysis on the NRT2 and NRT3 genes families across 132 plants (Sensu lato) to decipher their evolutionary history. We identified significant differences in the number of sequences per taxonomic group and different genomic contexts within the NRT2 family that might have contributed to N acquisition by the plants. We hypothesized that the greater losses of NRT2 sequences correlate with specialized ecological adaptations, such as aquatic, epiphytic, and carnivory lifestyles. We also detected expansion on the NRT2 family in specific lineages that could be a source of key innovations for colonizing contrasting niches in N availability. Microsyntenic analysis on NRT3 family showed a deep conservation on land plants, suggesting a high evolutionary constraint to preserve their function. Our study provides novel information that could be used as guide for functional characterization of these gene families across plant lineages.
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Affiliation(s)
- Normig M. Zoghbi-Rodríguez
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán A.C., Mérida 97205, Mexico;
| | - Samuel David Gamboa-Tuz
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán A.C., Mérida 97205, Mexico; (S.D.G.-T.); (L.C.R.-Z.)
| | - Alejandro Pereira-Santana
- Conacyt-Unidad de Biotecnología Industrial, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, Guadalajara 44270, Mexico;
| | - Luis C. Rodríguez-Zapata
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán A.C., Mérida 97205, Mexico; (S.D.G.-T.); (L.C.R.-Z.)
| | - Lorenzo Felipe Sánchez-Teyer
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán A.C., Mérida 97205, Mexico; (S.D.G.-T.); (L.C.R.-Z.)
| | - Ileana Echevarría-Machado
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán A.C., Mérida 97205, Mexico;
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18
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Nitrogen Assimilation Related Genes in Brassicanapus: Systematic Characterization and Expression Analysis Identified Hub Genes in Multiple Nutrient Stress Responses. PLANTS 2021; 10:plants10102160. [PMID: 34685969 PMCID: PMC8539475 DOI: 10.3390/plants10102160] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 09/30/2021] [Accepted: 10/02/2021] [Indexed: 11/17/2022]
Abstract
Nitrogen (N) is an essential macronutrient for plants. However, little is known about the molecular regulation of N assimilation in Brassica napus, one of the most important oil crops worldwide. Here, we carried out a comprehensive genome-wide analysis of the N assimilation related genes (NAGs) in B. napus. A total of 67 NAGs were identified encoding major enzymes involved in N assimilation, including asparagine synthetase (AS), glutamate dehydrogenase (GDH), glutamine oxoglutarate aminotransferase (GOGAT), glutamine synthetase (GS), nitrite reductase (NiR), nitrate reductase (NR). The syntenic analysis revealed that segmental duplication and whole-genome duplication were the main expansion pattern during gene evolution. Each NAG family showed different degrees of differentiation in characterization, gene structure, conserved motifs and cis-elements. Furthermore, diverse responses of NAG to multiple nutrient stresses were observed. Among them, more NAGs were regulated by N deficiency and ammonium toxicity than by phosphorus and potassium deprivations. Moreover, 12 hub genes responding to N starvation were identified, which may play vital roles in N utilization. Taken together, our results provide a basis for further functional research of NAGs in rapeseed N assimilation and also put forward new points in their responses to contrasting nutrient stresses.
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19
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Li S, Zhang H, Wang S, Shi L, Xu F, Wang C, Cai H, Ding G. The rapeseed genotypes with contrasting NUE response discrepantly to varied provision of ammonium and nitrate by regulating photosynthesis, root morphology, nutritional status, and oxidative stress response. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 166:348-360. [PMID: 34147727 DOI: 10.1016/j.plaphy.2021.06.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 06/01/2021] [Indexed: 06/12/2023]
Abstract
Ammonium (NH4+) and nitrate (NO3-) are the two predominant inorganic nitrogen (N) forms available to crops in agricultural soils. However, little is known about how the NH4+:NO3- ratio affect the growth of Brassica napus. Here, we investigated the impact of five NH4+:NO3- ratios (100:0, 75:25, 50:50, 25:75, 0:100) on plant growth, photosynthesis, root morphology, ammonium uptake, nutritional status, oxidative stress response, and relative expression of genes involved in these processes in two rapeseed genotypes with contrasting N use efficiency (NUE). Application of NO3- as a N source extremely improved rapeseed growth compare to NH4+. However, the best growth of the N-inefficient genotype was observed under 75:25 NH4+/NO3- ratio, while it happens for the N-efficient genotype only under the sole NO3- environment. The low-NUE genotype exhibited a more developed root system, higher photosynthetic capacity, higher nutrient accumulation, and better NH4+ uptake ability under the 75:25 NH4+/NO3- ratio, resulting in a decrease of malondialdehyde (MDA) in root. However, the high-NUE genotype performed better in the above aspects under the NO3--only condition. Nitrate decrease MDA by reducing the activities of superoxide dismutase, peroxidase, and catalase in root of the N-efficient genotype. Moreover, significant differences were detected for the expression levels of genes involved in N uptake and oxidative stress response between the two genotypes under two NH4+/NO3- ratios. Taken together, our results indicate that the N-inefficient rapeseed genotype prefers mixed supply of ammonium and nitrate, whereas the genotype with high NUE prefers sole nitrate environment.
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Affiliation(s)
- Shuang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China; Microelement Research Center / Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs / State Environmental Protection Key Laboratory of Soil Health and Green Remediation, Ministry of Ecology and Environment / College of Resources and Environment, Huazhong Agricultural University, 430070, Wuhan, China
| | - Hao Zhang
- Microelement Research Center / Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs / State Environmental Protection Key Laboratory of Soil Health and Green Remediation, Ministry of Ecology and Environment / College of Resources and Environment, Huazhong Agricultural University, 430070, Wuhan, China
| | - Sheliang Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China; Microelement Research Center / Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs / State Environmental Protection Key Laboratory of Soil Health and Green Remediation, Ministry of Ecology and Environment / College of Resources and Environment, Huazhong Agricultural University, 430070, Wuhan, China
| | - Lei Shi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China; Microelement Research Center / Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs / State Environmental Protection Key Laboratory of Soil Health and Green Remediation, Ministry of Ecology and Environment / College of Resources and Environment, Huazhong Agricultural University, 430070, Wuhan, China
| | - Fangsen Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China; Microelement Research Center / Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs / State Environmental Protection Key Laboratory of Soil Health and Green Remediation, Ministry of Ecology and Environment / College of Resources and Environment, Huazhong Agricultural University, 430070, Wuhan, China
| | - Chuang Wang
- Microelement Research Center / Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs / State Environmental Protection Key Laboratory of Soil Health and Green Remediation, Ministry of Ecology and Environment / College of Resources and Environment, Huazhong Agricultural University, 430070, Wuhan, China
| | - Hongmei Cai
- Microelement Research Center / Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs / State Environmental Protection Key Laboratory of Soil Health and Green Remediation, Ministry of Ecology and Environment / College of Resources and Environment, Huazhong Agricultural University, 430070, Wuhan, China
| | - Guangda Ding
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China; Microelement Research Center / Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs / State Environmental Protection Key Laboratory of Soil Health and Green Remediation, Ministry of Ecology and Environment / College of Resources and Environment, Huazhong Agricultural University, 430070, Wuhan, China.
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20
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Sun Q, Lu H, Zhang Q, Wang D, Chen J, Xiao J, Ding X, Li Q. Transcriptome sequencing of wild soybean revealed gene expression dynamics under low nitrogen stress. J Appl Genet 2021; 62:389-404. [PMID: 33770376 DOI: 10.1007/s13353-021-00628-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 02/25/2021] [Accepted: 03/08/2021] [Indexed: 01/22/2023]
Abstract
Nitrogen is one of the essential elements for plant growth. Wild soybeans (Glycine soja) have strong abilities to survive in harsh and barren environments, and hence become ideal plant model for studying plant adaptability to low nitrogen (LN) conditions. In this study, we analyzed and compared the transcriptomes of wild soybean subjected to LN treatments. We totally identified 1095 (681 up and 414 down) and 5490 (2998 up and 2492 down) differentially expressed genes (DEGs) in the aerial parts (leaf and stem, LS) and roots, respectively. Gene ontology classification analysis revealed that the categories related to LN stress (including oxidation reduction, transcriptional regulation, membrane, and protein phosphorylation) were highly enriched among DEGs. In addition, a total of 784 transcription factor (TF) and 84 transporter protein (TP) genes were determined in LS DEGs, of which some TF genes (NAC1, NAC35, ZFP1, CIM1, and WRKY25) and TP genes like NRT2.5 (nitrate transporter) and ABCC12 (ABC transporter) were widely upregulated under LN stress. Nevertheless, a total of 3859 TF and 370 TP genes were identified in root DEGs, of which some TF genes (NAC6, NAC14, MYB29, MYB92, bZIP62, bZIP72, WRKY60, WRKY58) and TP genes like NRT2.4 and HAK5 (potassium transporter) were upregulated under LN stress. These findings suggest that the identified DEGs may play vital roles in plant responses to LN stress, providing important genetic resources for further functional dissection of plant molecular mechanisms to LN stress.
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Affiliation(s)
- Qi Sun
- Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin, 150030, China
| | - Haoran Lu
- Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin, 150030, China
| | - Qing Zhang
- Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin, 150030, China
| | - Di Wang
- Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin, 150030, China
| | - Jun Chen
- Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin, 150030, China
| | - Jialei Xiao
- Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin, 150030, China
| | - Xiaodong Ding
- Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin, 150030, China.
| | - Qiang Li
- Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin, 150030, China.
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21
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Transcriptome Analysis of Two Near-Isogenic Lines with Different NUE under Normal Nitrogen Conditions in Wheat. BIOLOGY 2021; 10:biology10080787. [PMID: 34440020 PMCID: PMC8389668 DOI: 10.3390/biology10080787] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/11/2021] [Accepted: 08/14/2021] [Indexed: 02/06/2023]
Abstract
Simple Summary High nitrogen use efficiency (NUE) in wheat (Triticum aestivum L.) is the key to ensure high yield and reduce pollution. Understanding the physiological and molecular changes that regulate NUE is important for the breeding of high-NUE wheat varieties. Carbon and nitrogen metabolism are the basic metabolic pathways in plants. It becomes important to reveal the underlying molecular mechanisms related to carbon and nitrogen metabolism, which may be helpful to improve NUE. In this paper, two wheat near-isogenic lines (NILs) with contrasting NUE were performed RNA-Sequencing (RNA-Seq) to identify candidate genes associated with carbon/nitrogen metabolism under normal nitrogen conditions. Our research may provide new insights into the comprehensive understanding of the molecular mechanism underlying NUE. Abstract Nitrogen (N) is an essential nutrient element for crop productivity. Unfortunately, the nitrogen use efficiency (NUE) of crop plants gradually decreases with the increase of the N application rate. Nevertheless, little has been known about the molecular mechanisms of differences in NUE among genotypes of wheat. In this study, we used RNA-Sequencing (RNA-Seq) to compare the transcriptome profiling of flag leaves at the stage of anthesis in wheat NILs (1Y, high-NUE, and 1W, low-NUE) under normal nitrogen conditions (300 kg N ha−1, corresponding to 1.6 g N pot−1). We identified 7023 DEGs (4738 upregulated and 2285 downregulated) in the comparison between lines 1Y and 1W. The responses of 1Y and 1W to normal N differed in the transcriptional regulatory mechanisms. Several genes belonging to the GS and GOGAT gene families were upregulated in 1Y compared with 1W, and the enhanced carbon metabolism might lead 1Y to produce more C skeletons, metabolic energy, and reductants for nitrogen metabolism. A subset of transcription factors (TFs) family members, such as ERF, WRKY, NAC, and MYB, were also identified. Collectively, these identified candidate genes provided new information for a further understanding of the genotypic difference in NUE.
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Huo L, Guo Z, Wang Q, Cheng L, Jia X, Wang P, Gong X, Li C, Ma F. Enhanced Autophagic Activity Improved the Root Growth and Nitrogen Utilization Ability of Apple Plants under Nitrogen Starvation. Int J Mol Sci 2021; 22:ijms22158085. [PMID: 34360850 PMCID: PMC8348665 DOI: 10.3390/ijms22158085] [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: 06/26/2021] [Revised: 07/15/2021] [Accepted: 07/20/2021] [Indexed: 12/26/2022] Open
Abstract
Autophagy is a conserved degradation pathway for recycling damaged organelles and aberrant proteins, and its important roles in plant adaptation to nutrient starvation have been generally reported. Previous studies found that overexpression of autophagy-related (ATG) gene MdATG10 enhanced the autophagic activity in apple roots and promoted their salt tolerance. The MdATG10 expression was induced by nitrogen depletion condition in both leaves and roots of apple plants. This study aimed to investigate the differences in the growth and physiological status between wild type and MdATG10-overexpressing apple plants in response to nitrogen starvation. A hydroponic system containing different nitrogen levels was used. The study found that the reduction in growth and nitrogen concentrations in different tissues caused by nitrogen starvation was relieved by MdATG10 overexpression. Further studies demonstrated the increased root growth and the higher nitrogen absorption and assimilation ability of transgenic plants. These characteristics contributed to the increased uptake of limited nitrogen nutrients by transgenic plants, which also reduced the starvation damage to the chloroplasts. Therefore, the MdATG10-overexpressing apple plants could maintain higher photosynthetic ability and possess better growth under nitrogen starvation stress.
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Affiliation(s)
- Liuqing Huo
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Shaanxi 712100, China; (L.H.); (Z.G.); (Q.W.); (L.C.); (X.J.); (P.W.); (X.G.)
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas, College of Horticulture Science, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
| | - Zijian Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Shaanxi 712100, China; (L.H.); (Z.G.); (Q.W.); (L.C.); (X.J.); (P.W.); (X.G.)
| | - Qi Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Shaanxi 712100, China; (L.H.); (Z.G.); (Q.W.); (L.C.); (X.J.); (P.W.); (X.G.)
| | - Li Cheng
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Shaanxi 712100, China; (L.H.); (Z.G.); (Q.W.); (L.C.); (X.J.); (P.W.); (X.G.)
| | - Xin Jia
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Shaanxi 712100, China; (L.H.); (Z.G.); (Q.W.); (L.C.); (X.J.); (P.W.); (X.G.)
| | - Ping Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Shaanxi 712100, China; (L.H.); (Z.G.); (Q.W.); (L.C.); (X.J.); (P.W.); (X.G.)
| | - Xiaoqing Gong
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Shaanxi 712100, China; (L.H.); (Z.G.); (Q.W.); (L.C.); (X.J.); (P.W.); (X.G.)
| | - Cuiying Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Shaanxi 712100, China; (L.H.); (Z.G.); (Q.W.); (L.C.); (X.J.); (P.W.); (X.G.)
- Correspondence: (C.L.); (F.M.)
| | - Fengwang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Shaanxi 712100, China; (L.H.); (Z.G.); (Q.W.); (L.C.); (X.J.); (P.W.); (X.G.)
- Correspondence: (C.L.); (F.M.)
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Meng X, Wang X, Zhang Z, Xiong S, Wei Y, Guo J, Zhang J, Wang L, Ma X, Tegeder M. Transcriptomic, proteomic, and physiological studies reveal key players in wheat nitrogen use efficiency under both high and low nitrogen supply. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:4435-4456. [PMID: 33829261 DOI: 10.1093/jxb/erab153] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 04/02/2021] [Indexed: 06/12/2023]
Abstract
The effective use of available nitrogen (N) to improve crop grain yields provides an important strategy to reduce environmental N pollution and promote sustainable agriculture. However, little is known about the common genetic basis of N use efficiency (NUE) at varying N availability. Two wheat (Triticum aestivum L.) cultivars were grown in the field with high, moderate, and low N supply. Cultivar Zhoumai 27 outperformed Aikang 58 independent of the N supply and showed improved growth, canopy leaf area index, flag leaf surface area, grain number, and yield, and enhanced NUE due to both higher N uptake and utilization efficiency. Further, transcriptome and proteome analyses were performed using flag leaves that provide assimilates for grain growth. The results showed that many genes or proteins that are up- or down-regulated under all N regimes are associated with N and carbon metabolism and transport. This was reinforced by cultivar differences in photosynthesis, assimilate phloem transport, and grain protein/starch yield. Overall, our study establishes that improving NUE at both high and low N supply requires distinct adjustments in leaf metabolism and assimilate partitioning. Identified key genes/proteins may individually or concurrently regulate NUE and are promising targets for maximizing crop NUE irrespective of the N supply.
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Affiliation(s)
- Xiaodan Meng
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, ZhengzhouChina
- College of Agronomy, Henan Agricultural University, ZhengzhouChina
- School of Biological Sciences, Washington State University, Pullman, WAUSA
| | - Xiaochun Wang
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, ZhengzhouChina
| | - Zhiyong Zhang
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, ZhengzhouChina
- College of Agronomy, Henan Agricultural University, ZhengzhouChina
| | - Shuping Xiong
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, ZhengzhouChina
- College of Agronomy, Henan Agricultural University, ZhengzhouChina
| | - Yihao Wei
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, ZhengzhouChina
- College of Agronomy, Henan Agricultural University, ZhengzhouChina
| | - Jianbiao Guo
- College of Agronomy, Henan Agricultural University, ZhengzhouChina
| | - Jie Zhang
- College of Agronomy, Henan Agricultural University, ZhengzhouChina
| | - Lulu Wang
- College of Agronomy, Henan Agricultural University, ZhengzhouChina
| | - Xinming Ma
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, ZhengzhouChina
- College of Agronomy, Henan Agricultural University, ZhengzhouChina
| | - Mechthild Tegeder
- School of Biological Sciences, Washington State University, Pullman, WAUSA
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24
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Roch GV, Maharajan T, Krishna TPA, Ignacimuthu S, Ceasar SA. Expression of PHT1 family transporter genes contributes for low phosphate stress tolerance in foxtail millet (Setaria italica) genotypes. PLANTA 2020; 252:98. [PMID: 33159589 DOI: 10.1007/s00425-020-03503-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 10/23/2020] [Indexed: 05/27/2023]
Abstract
This is a first comprehensive study to analyze the 12 PHT1 family phosphate transporter genes in 20 foxtail millet genotypes for the improvement of millets and other crops for phosphate use efficiency. Phosphorus (P), absorbed from soil solutions as inorganic phosphate (Pi), is a limiting nutrient for plant growth and yield. Twenty genotypes of foxtail millet (Setaria italica) with contrasting degree of growth and Pi uptake responses under low Pi (LP) and high Pi (HP) supply were chosen based on a previous study. To gain molecular insights, expression dynamics of 12 PHosphate Transporter 1 (PHT1) family (SiPHT1;1 to 1;12) genes were analyzed in these 20 genotypes and compared with their Pi and total P (TP) contents. SiPHT1;1, 1;2, 1;3 and 1;8 genes were expressed in shoot tissues of three (ISe 1209, ISe 1305 and Co-6) of the LP best performing genotypes (LPBG); however, they were expressed in only one of the LP worst performing genotype (LPWG) (ISe 748). More importantly, this is correlating with higher shoot Pi and TP contents of the LPBG compared to LPWG. Apart from this condition, expression of SiPHT1 genes and their Pi and TP contents do not correlate directly for many genotypes in other conditions; genotypes with low Pi and TP contents induced more SiPHT1 genes and vice versa. Promoter analysis revealed that genotype ISe 1888 with a high level of SiPHT1;8 expression possesses two additional root box motifs compared to other genotypes. The PHT1 family genes seem to play a key role for LP stress tolerance in foxtail millet and further studies will help to improve the P-use efficiency in foxtail millet and other cereals.
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Affiliation(s)
- G Victor Roch
- Division of Plant Biotechnology, Entomology Research Institute, Loyola College, Chennai, 600034, India
| | - T Maharajan
- Division of Plant Biotechnology, Entomology Research Institute, Loyola College, Chennai, 600034, India
| | - T P Ajeesh Krishna
- Division of Plant Biotechnology, Entomology Research Institute, Loyola College, Chennai, 600034, India
| | - S Ignacimuthu
- Xavier Research Foundation, St Xavier's College, Palayamkottai, India
| | - S Antony Ceasar
- Division of Plant Biotechnology, Entomology Research Institute, Loyola College, Chennai, 600034, India.
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25
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Tong J, Walk TC, Han P, Chen L, Shen X, Li Y, Gu C, Xie L, Hu X, Liao X, Qin L. Genome-wide identification and analysis of high-affinity nitrate transporter 2 (NRT2) family genes in rapeseed (Brassica napus L.) and their responses to various stresses. BMC PLANT BIOLOGY 2020; 20:464. [PMID: 33036562 PMCID: PMC7547492 DOI: 10.1186/s12870-020-02648-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 09/14/2020] [Indexed: 05/22/2023]
Abstract
BACKGROUND High-affinity nitrate transporter 2 (NRT2) genes have been implicated in nitrate absorption and remobilization under nitrogen (N) starvation stress in many plant species, yet little is known about this gene family respond to various stresses often occurs in the production of rapeseed (Brassica napus L.). RESULTS This report details identification of 17 NRT2 gene family members in rapeseed, as well as, assessment of their expression profiles using RNA-seq analysis and qRT-PCR assays. In this study, all BnNRT2.1 members, BnNRT2.2a and BnNRT2.4a were specifically expressed in root tissues, while BnNRT2.7a and BnNRT2.7b were mainly expressed in aerial parts, including as the predominantly expressed NRT2 genes detected in seeds. This pattern of shoot NRT expression, along with homology to an Arabidopsis NRT expressed in seeds, strongly suggests that both BnNRT2.7 genes play roles in seed nitrate accumulation. Another rapeseed NRT, BnNRT2.5 s, exhibited intermediate expression, with transcripts detected in both shoot and root tissues. Functionality of BnNRT2s genes was further outlined by testing for adaptive responses in expression to exposure to a series of environmental stresses, including N, phosphorus (P) or potassium (K) deficiency, waterlogging and drought. In these tests, most NRT2 gene members were up-regulated by N starvation and restricted by the other stresses tested herein. In contrast to this overall trend, transcription of BnNRT2.1a was up-regulated under waterlogging and K deficiency stress, and BnNRT2.5 s was up-regulated in roots subjected to waterlogging. Furthermore, the mRNA levels of BnNRT2.7 s were enhanced under both waterlogging stress and P or K deficiency conditions. These results suggest that these three BnNRT2 genes might participate in crosstalk among different stress response pathways. CONCLUSIONS The results presented here outline a diverse set of NRT2 genes present in the rapeseed genome that collectively carry out specific functions throughout rapeseed development, while also responding not just to N deficiency, but also to several other stresses. Targeting of individual BnNRT2 members that coordinate rapeseed nitrate uptake and transport in response to cues from multiple stress response pathways could significantly expand the genetic resources available for improving rapeseed resistance to environmental stresses.
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Affiliation(s)
- Jiafeng Tong
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetics Improvement of Oil Crops of the Ministry of Agriculture and Rural Affairs, Wuhan, 430062, P. R. China
| | | | - Peipei Han
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetics Improvement of Oil Crops of the Ministry of Agriculture and Rural Affairs, Wuhan, 430062, P. R. China
- Institute of Agriculture Science in Jiangsu Coastal Area, Yancheng, 224002, P. R. China
| | - Liyu Chen
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, P. R. China
| | - Xinjie Shen
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetics Improvement of Oil Crops of the Ministry of Agriculture and Rural Affairs, Wuhan, 430062, P. R. China
| | - Yinshui Li
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetics Improvement of Oil Crops of the Ministry of Agriculture and Rural Affairs, Wuhan, 430062, P. R. China
| | - Chiming Gu
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetics Improvement of Oil Crops of the Ministry of Agriculture and Rural Affairs, Wuhan, 430062, P. R. China
| | - Lihua Xie
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetics Improvement of Oil Crops of the Ministry of Agriculture and Rural Affairs, Wuhan, 430062, P. R. China
| | - Xiaojia Hu
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetics Improvement of Oil Crops of the Ministry of Agriculture and Rural Affairs, Wuhan, 430062, P. R. China
| | - Xing Liao
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetics Improvement of Oil Crops of the Ministry of Agriculture and Rural Affairs, Wuhan, 430062, P. R. China.
| | - Lu Qin
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetics Improvement of Oil Crops of the Ministry of Agriculture and Rural Affairs, Wuhan, 430062, P. R. China.
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Genome-Wide Systematic Characterization of the NPF Family Genes and Their Transcriptional Responses to Multiple Nutrient Stresses in Allotetraploid Rapeseed. Int J Mol Sci 2020; 21:ijms21175947. [PMID: 32824914 PMCID: PMC7504168 DOI: 10.3390/ijms21175947] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 08/13/2020] [Accepted: 08/17/2020] [Indexed: 12/19/2022] Open
Abstract
NITRATE TRANSPORTER 1 (NRT1)/PEPTIDE TRANSPORTER (PTR) family (NPF) proteins can transport various substrates, and play crucial roles in governing plant nitrogen (N) uptake and distribution. However, little is known about the NPF genes in Brassica napus. Here, a comprehensive genome-wide systematic characterization of the NPF family led to the identification of 193 NPF genes in the whole genome of B. napus. The BnaNPF family exhibited high levels of genetic diversity among sub-families but this was conserved within each subfamily. Whole-genome duplication and segmental duplication played a major role in BnaNPF evolution. The expression analysis indicated that a broad range of expression patterns for individual gene occurred in response to multiple nutrient stresses, including N, phosphorus (P) and potassium (K) deficiencies, as well as ammonium toxicity. Furthermore, 10 core BnaNPF genes in response to N stress were identified. These genes contained 6–13 transmembrane domains, located in plasma membrane, that respond discrepantly to N deficiency in different tissues. Robust cis-regulatory elements were identified within the promoter regions of the core genes. Taken together, our results suggest that BnaNPFs are versatile transporters that might evolve new functions in B. napus. Our findings benefit future research on this gene family.
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