1
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Wang H, Wang W, Xie Z, Yang Y, Dai H, Shi F, Ma L, Sui Z, Xia C, Kong X, Zhang L. Overexpression of rice OsNRT1.1A/OsNPF6.3 enhanced the nitrogen use efficiency of wheat under low nitrogen conditions. PLANTA 2024; 259:127. [PMID: 38637411 DOI: 10.1007/s00425-024-04408-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 04/04/2024] [Indexed: 04/20/2024]
Abstract
MAIN CONCLUSION Overexpression of OsNRT1.1A promotes early heading and increases the tolerance in wheat under nitrogen deficiency conditions. The application of inorganic nitrogen (N) fertilizers is a major driving force for crop yield improvement. However, the overuse of fertilizers significantly raises production costs and leads to environmental problems, making it critical to enhance crop nitrogen use efficiency (NUE) for the sake of sustainable agriculture. In this study, we created a series of transgenic wheat lines carrying the rice OsNRT1.1A gene, which encodes a nitrate transporter, to investigate its possible application in improving NUE in wheat. The transgenic wheat exhibited traits such as early maturation that were highly consistent with the overexpression of OsNRT1.1A in Arabidopsis and rice. However, we also observed that overexpression of the OsNRT1.1A gene in wheat can facilitate the growth of roots under low N conditions but has no effect on other aspects of growth and development under normal N conditions. Thus, it may lead to the improvement of wheat low N tolerance,which is different from the effects reported in other plants. A field trial analysis showed that transgenic wheat exhibited increased grain yield per plant under low N conditions. Moreover, transcriptome analysis indicated that OsNRT1.1A increased the expression levels of N uptake and utilization genes in wheat, thereby promoting plant growth under low N conditions. Taken together, our results indicated that OsNRT1.1A plays an important role in improving NUE in wheat with low N availability.
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Affiliation(s)
- Huanhuan Wang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Wei Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Zhencheng Xie
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yuxin Yang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hongyong Dai
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Feng Shi
- Laboratory of Shijiazhuang Academy of Agricultural and Forestry Sciences, Shijiazhuang Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050000, China
| | - Liang Ma
- Laboratory of Shijiazhuang Academy of Agricultural and Forestry Sciences, Shijiazhuang Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050000, China
| | - Zhifeng Sui
- Laboratory of Shijiazhuang Academy of Agricultural and Forestry Sciences, Shijiazhuang Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050000, China
| | - Chuan Xia
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiuying Kong
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Lichao Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Parveen K, Saddique MAB, Ali Z, Ur Rehman S, Zaib-Un-Nisa, Khan Z, Waqas M, Munir MZ, Hussain N, Muneer MA. Genome-wide analysis of Glutathione peroxidase (GPX) gene family in Chickpea (Cicer arietinum L.) under salinity stress. Gene 2024; 898:148088. [PMID: 38104951 DOI: 10.1016/j.gene.2023.148088] [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: 09/11/2023] [Revised: 11/23/2023] [Accepted: 12/13/2023] [Indexed: 12/19/2023]
Abstract
Chickpea is the second most widely grown legume in the world. Its cultivation is highly affected by saline soils. Salt stress damages its all growth stages from germination to maturity. It has a huge genetic diversity containing adaptation loci that can help produce salt-tolerant cultivars. The glutathione peroxidase (GPX) gene family plays an important role in regulating plant response to abiotic stimuli and protects cells from oxidative damage. In current research, the role of GPX genes is studied for inducing salt tolerance in chickpea. This study identifies the GPX gene family in Cicer arietinum. In response to the NaCl stress, the gene expression profiles of CaGPX3 were examined using real-time qRT-PCR. The results of phylogenetic analysis show that CaGPX genes have an evolutionary relationship with monocots, dicots, chlorophytes, and angiosperms. Gene structure analysis showed that CaGPX3, CaGPX4, and CaGPX5 have six, CaGPX2 has five, and CaGPX1 contains 9 exons. According to the Ka and Ks analysis chickpea has one pair of duplicated genes of GPX and the duplication was tandem with negative (purifying) selection Ka < Ks (<1). In-silico gene expression analysis revealed that CaGPX3 is a salt stress-responsive gene among all other five GPX members in chickpea. The qRT-PCR results showed that the CaGPX3 gene expression was co-ordinately regulated under salt stress conditions, confirming CaGPX3's key involvement in salt tolerance.
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Affiliation(s)
- Kauser Parveen
- Institute of Plant Breeding and Biotechnology, MNS University of Agriculture Multan, Pakistan
| | | | - Zulfiqar Ali
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan; Programs and Projects Department, Islamic Organization for Food Security, Astana, Kazakhstan
| | - Shoaib Ur Rehman
- Institute of Plant Breeding and Biotechnology, MNS University of Agriculture Multan, Pakistan; SINO-PAK Joint Research Laboratory, Institute of Plant Breeding and Biotechnology, MNS University of Agriculture Multan, Pakistan.
| | - Zaib-Un-Nisa
- Cotton Research Institute, Multan, Punjab, Pakistan
| | - Zulqurnain Khan
- Institute of Plant Breeding and Biotechnology, MNS University of Agriculture Multan, Pakistan
| | - Muhammad Waqas
- Pakistan Agricultural Research Council, Arid Zone Research Center, Pakistan Agricultural Research Council, Dera Ismail Khan, Pakistan
| | - Muhammad Zeeshan Munir
- School of Environment and Energy, Peking University Shenzhen Graduate School, 2199 Lishui Rd., Shenzhen 518055, China
| | - Niaz Hussain
- Arid Zone Research Institute Bhakkar, Punjab, Pakistan
| | - Muhammad Atif Muneer
- International Magnesium Institute, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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3
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Li Q, Song HL, Zhou T, Pei MN, Wang B, Yan SX, Liu YQ, Wu PJ, Hua YP. Differential Morpho-Physiological, Ionomic, and Phytohormone Profiles, and Genome-Wide Expression Profiling Involving the Tolerance of Allohexaploid Wheat ( Triticum aestivum L.) to Nitrogen Limitation. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:3814-3831. [PMID: 38329036 DOI: 10.1021/acs.jafc.3c08626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Common wheat (Triticum aestivum L.) is a global staple food, while nitrogen (N) limitation severely hinders plant growth, seed yield, and grain quality of wheat. Genetic variations in the responses to low N stresses among allohexaploid wheat (AABBDD, 2n = 6x = 42) genotypes emphasize the complicated regulatory mechanisms underlying low N tolerance and N use efficiency (NUE). In this study, hydroponic culture, inductively coupled plasma mass spectrometry, noninvasive microtest, high-performance liquid chromatography, RNA-seq, and bioinformatics were used to determine the differential growth performance, ionome and phytohormone profiles, and genome-wide expression profiling of wheat plants grown under high N and low N conditions. Transcriptional profiling of NPFs, NRT2s, CLCs, SLACs/SLAHs, AAPs, UPSs, NIAs, and GSs characterized the core members, such as TaNPF6.3-6D, TaNRT2.3-3D, TaNIA1-6B, TaGLN1;2-4B, TaAAP14-5A/5D, and TaUPS2-5A, involved in the efficient transport and assimilation of nitrate and organic N nutrients. The low-N-sensitivity wheat cultivar XM26 showed obvious leaf chlorosis and accumulated higher levels of ABA, JA, and SA than the low-N-tolerant ZM578 under N limitation. The TaMYB59-3D-TaNPF7.3/NRT1.5-6D module-mediated shoot-to-root translocation and leaf remobilization of nitrate was proposed as an important pathway regulating the differential responses between ZM578 and XM26 to low N. This study provides some elite candidate genes for the selection and breeding of wheat germplasms with low N tolerance and high NUE.
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Affiliation(s)
- Qiong Li
- Department of Brewing Engineering, Moutai Institute, Renhuai 564507, Guizhou, China
| | - Hai-Li Song
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Ting Zhou
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Min-Nan Pei
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Bing Wang
- Department of Brewing Engineering, Moutai Institute, Renhuai 564507, Guizhou, China
| | - Song-Xian Yan
- Department of Resources and Environment, Moutai Institute, Renhuai 564507, Guizhou, China
| | - Yun-Qi Liu
- Zhongguancun Xuyue Non-invasive Micro-test Technology Industrial Alliance, Beijing 10080, China
| | - Peng-Jia Wu
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Ying-Peng Hua
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
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4
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Santin A, Russo MT, de Los Ríos LM, Chiurazzi M, d'Alcalà MR, Lacombe B, Ferrante MI, Rogato A. The tonoplast localized protein PtNPF1 participates in the regulation of nitrogen response in diatoms. THE NEW PHYTOLOGIST 2024; 241:1592-1604. [PMID: 38084038 DOI: 10.1111/nph.19461] [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: 10/26/2023] [Accepted: 11/21/2023] [Indexed: 01/26/2024]
Abstract
Diatoms are a highly successful group of phytoplankton, well adapted also to oligotrophic environments and capable of handling nutrient fluctuations in the ocean, particularly nitrate. The presence of a large vacuole is an important trait contributing to their adaptive features. It confers diatoms the ability to accumulate and store nutrients, such as nitrate, when they are abundant outside and then to reallocate them into the cytosol to meet deficiencies, in a process called luxury uptake. The molecular mechanisms that regulate these nitrate fluxes are still not known in diatoms. In this work, we provide new insights into the function of Phaeodactylum tricornutum NPF1, a putative low-affinity nitrate transporter. To accomplish this, we generated overexpressing strains and CRISPR/Cas9 loss-of-function mutants. Microscopy observations confirmed predictions that PtNPF1 is localized on the vacuole membrane. Furthermore, functional characterizations performed on knock-out mutants revealed a transient growth delay phenotype linked to altered nitrate uptake. Together, these results allowed us to hypothesize that PtNPF1 is presumably involved in modulating intracellular nitrogen fluxes, managing intracellular nutrient availability. This ability might allow diatoms to fine-tune the assimilation, storage and reallocation of nitrate, conferring them a strong advantage in oligotrophic environments.
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Affiliation(s)
- Anna Santin
- Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, 80121, Italy
| | | | - Laura Morales de Los Ríos
- Institute for Plant Science of Montpellier (IPSiM), University of Montpellier, CNRS, INRAE, Montpellier SupAgro, Place Pierre Viala 2, Montpellier, 34060, France
| | - Maurizio Chiurazzi
- Institute of Biosciences and BioResources, CNR, Via P. Castellino 111, Naples, 80131, Italy
| | | | - Benoît Lacombe
- Institute for Plant Science of Montpellier (IPSiM), University of Montpellier, CNRS, INRAE, Montpellier SupAgro, Place Pierre Viala 2, Montpellier, 34060, France
| | - Maria Immacolata Ferrante
- Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, 80121, Italy
- National Institute of Oceanography and Applied Geophysics, Trieste, 34010, Italy
| | - Alessandra Rogato
- Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, 80121, Italy
- Institute of Biosciences and BioResources, CNR, Via P. Castellino 111, Naples, 80131, Italy
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5
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Sigalas PP, Buchner P, Kröper A, Hawkesford MJ. The Functional Diversity of the High-Affinity Nitrate Transporter Gene Family in Hexaploid Wheat: Insights from Distinct Expression Profiles. Int J Mol Sci 2023; 25:509. [PMID: 38203680 PMCID: PMC10779101 DOI: 10.3390/ijms25010509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 12/22/2023] [Accepted: 12/23/2023] [Indexed: 01/12/2024] Open
Abstract
High-affinity nitrate transporters (NRT) are key components for nitrogen (N) acquisition and distribution within plants. However, insights on these transporters in wheat are scarce. This study presents a comprehensive analysis of the NRT2 and NRT3 gene families, where the aim is to shed light on their functionality and to evaluate their responses to N availability. A total of 53 NRT2s and 11 NRT3s were identified in the bread wheat genome, and these were grouped into different clades and homoeologous subgroups. The transcriptional dynamics of the identified NRT2 and NRT3 genes, in response to N starvation and nitrate resupply, were examined by RT-qPCR in the roots and shoots of hydroponically grown wheat plants through a time course experiment. Additionally, the spatial expression patterns of these genes were explored within the plant. The NRT2s of clade 1, TaNRT2.1-2.6, showed a root-specific expression and significant upregulation in response to N starvation, thus emphasizing a role in N acquisition. However, most of the clade 2 NRT2s displayed reduced expression under N-starved conditions. Nitrate resupply after N starvation revealed rapid responsiveness in TaNRT2.1-2.6, while clade 2 genes exhibited gradual induction, primarily in the roots. TaNRT2.18 was highly expressed in above-ground tissues and exhibited distinct nitrate-related response patterns for roots and shoots. The TaNRT3 gene expression closely paralleled the profiles of TaNRT2.1-2.6 in response to nitrate induction. These findings enhance the understanding of NRT2 and NRT3 involvement in nitrogen uptake and utilization, and they could have practical implications for improving nitrogen use efficiency. The study also recommends a standardized nomenclature for wheat NRT2 genes, thereby addressing prior naming inconsistencies.
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Affiliation(s)
- Petros P. Sigalas
- Rothamsted Research, West Common, Harpenden AL5 2JQ, UK; (P.B.); (M.J.H.)
| | - Peter Buchner
- Rothamsted Research, West Common, Harpenden AL5 2JQ, UK; (P.B.); (M.J.H.)
| | - Alex Kröper
- Faculty of Agronomy, University of Hohenheim, 70599 Stuttgart, Germany;
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6
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Wang J, Wang L, Zhang X, Li S, Wang X, Yang L, Wu F, Su H. Genome-wide identification of nitrate transporter 1/peptide transporter family (NPF) genes reveals that PaNPF5.5 enhances nitrate uptake in sweet cherry under high nitrate condition. Gene 2023; 888:147797. [PMID: 37708922 DOI: 10.1016/j.gene.2023.147797] [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: 07/17/2023] [Revised: 09/10/2023] [Accepted: 09/11/2023] [Indexed: 09/16/2023]
Abstract
NITRATE TRANSPORTER 1 (NRT1)/PEPTIDETRANSPORTER (PTR) family (NPF) plays a significant role in nitrate transport. However, little is known about the NPF genes in sweet cherry. In this study, a total of 60 PaNPF genes in sweet cherry were identified by bioinformatics, which were divided into 8 families. Transcriptomic analysis showed that most PaNPF genes responded to both low and high nitrate conditions, especially PaNPF5.5, which was highly up-regulated under high nitrate condition. Molecular analysis showed that PaNPF5.5 was a transporter localized to the cell membrane. Further functional studies found that PaNPF5.5 overexpression promoted the growth of sweet cherry rootstock Gisela 6 by accelerating the nitrogen absorption process under high nitrate environment. Taken together, we believe that PaNPF5.5 plays an important role in regulating the transport of nitrate at high nitrate conditions, and provides a promising method for improving nitrate absorption efficiency at nitrogen excess environment.
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Affiliation(s)
- Jingtao Wang
- School of Agriculture, Ludong University, Yantai 264025, China; College of Life Sciences, Ludong University, Yantai 264025, China
| | - Lei Wang
- College of Life Sciences, Ludong University, Yantai 264025, China
| | - Xu Zhang
- Yantai Academy of Agricultural Sciences, Yantai, Shandong 264025, China
| | - Songlin Li
- School of Agriculture, Ludong University, Yantai 264025, China
| | - Xiaohui Wang
- School of Agriculture, Ludong University, Yantai 264025, China
| | - Lina Yang
- Department of Genetics and Cell Biology, Basic Medical College, Qingdao University, Qingdao 266071, China
| | - Fanlin Wu
- School of Agriculture, Ludong University, Yantai 264025, China.
| | - Hongyan Su
- College of Agriculture and Forestry Sciences, Linyi University, Linyi 276000, China.
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7
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Puccio G, Ingraffia R, Giambalvo D, Frenda AS, Harkess A, Sunseri F, Mercati F. Exploring the genetic landscape of nitrogen uptake in durum wheat: genome-wide characterization and expression profiling of NPF and NRT2 gene families. FRONTIERS IN PLANT SCIENCE 2023; 14:1302337. [PMID: 38023895 PMCID: PMC10665861 DOI: 10.3389/fpls.2023.1302337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 10/25/2023] [Indexed: 12/01/2023]
Abstract
Nitrate uptake by plants primarily relies on two gene families: Nitrate transporter 1/peptide transporter (NPF) and Nitrate transporter 2 (NRT2). Here, we extensively characterized the NPF and NRT2 families in the durum wheat genome, revealing 211 NPF and 20 NRT2 genes. The two families share many Cis Regulatory Elements (CREs) and Transcription Factor binding sites, highlighting a partially overlapping regulatory system and suggesting a coordinated response for nitrate transport and utilization. Analyzing RNA-seq data from 9 tissues and 20 cultivars, we explored expression profiles and co-expression relationships of both gene families. We observed a strong correlation between nucleotide variation and gene expression within the NRT2 gene family, implicating a shared selection mechanism operating on both coding and regulatory regions. Furthermore, NPF genes showed highly tissue-specific expression profiles, while NRT2s were mainly divided in two co-expression modules, one expressed in roots (NAR2/NRT3 dependent) and the other induced in anthers and/ovaries during maturation. Our evidences confirmed that the majority of these genes were retained after small-scale duplication events, suggesting a neo- or sub-functionalization of many NPFs and NRT2s. Altogether, these findings indicate that the expansion of these gene families in durum wheat could provide valuable genetic variability useful to identify NUE-related and candidate genes for future breeding programs in the context of low-impact and sustainable agriculture.
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Affiliation(s)
- Guglielmo Puccio
- Department of Agricultural, Food and Forestry Sciences, University of Palermo, Palermo, Italy
- Institute of Biosciences and BioResources (IBBR), National Research Council, Palermo, Italy
| | - Rosolino Ingraffia
- Department of Agricultural, Food and Forestry Sciences, University of Palermo, Palermo, Italy
| | - Dario Giambalvo
- Department of Agricultural, Food and Forestry Sciences, University of Palermo, Palermo, Italy
| | - Alfonso S. Frenda
- Department of Agricultural, Food and Forestry Sciences, University of Palermo, Palermo, Italy
| | - Alex Harkess
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Francesco Sunseri
- Institute of Biosciences and BioResources (IBBR), National Research Council, Palermo, Italy
- Department Agraria , University Mediterranea of Reggio Calabria, Reggio Calabria, Italy
| | - Francesco Mercati
- Institute of Biosciences and BioResources (IBBR), National Research Council, Palermo, Italy
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8
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Bekele-Alemu A, Ligaba-Osena A. Comprehensive in silico analysis of the underutilized crop tef (Eragrostis tef (Zucc.) Trotter) genome reveals drought tolerance signatures. BMC PLANT BIOLOGY 2023; 23:506. [PMID: 37865758 PMCID: PMC10589971 DOI: 10.1186/s12870-023-04515-1] [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: 04/20/2023] [Accepted: 10/05/2023] [Indexed: 10/23/2023]
Abstract
BACKGROUND Tef (Eragrostis tef) is a C4 plant known for its tiny, nutritious, and gluten-free grains. It contains higher levels of protein, vitamins, and essential minerals like calcium (Ca), iron (Fe), copper (Cu), and zinc (Zn) than common cereals. Tef is cultivated in diverse ecological zones under diverse climatic conditions. Studies have shown that tef has great diversity in withstanding environmental challenges such as drought. Drought is a major abiotic stress severely affecting crop productivity and becoming a bottleneck to global food security. Here, we used in silico-based functional genomic analysis to identify drought-responsive genes in tef and validated their expression using quantitative RT-PCR. RESULTS We identified about 729 drought-responsive genes so far reported in six crop plants, including rice, wheat, maize, barley, sorghum, pearl millet, and the model plant Arabidopsis, and reported 20 genes having high-level of GO terms related to drought, and significantly enriched in several biological and molecular function categories. These genes were found to play diverse roles, including water and fluid transport, resistance to high salt, cold, and drought stress, abscisic acid (ABA) signaling, de novo DNA methylation, and transcriptional regulation in tef and other crops. Our analysis revealed substantial differences in the conserved domains of some tef genes from well-studied rice orthologs. We further analyzed the expression of sixteen tef orthologs using quantitative RT-PCR in response to PEG-induced osmotic stress. CONCLUSIONS The findings showed differential regulation of some drought-responsive genes in shoots, roots, or both tissues. Hence, the genes identified in this study may be promising candidates for trait improvement in crops via transgenic or gene-editing technologies.
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Affiliation(s)
- Abreham Bekele-Alemu
- Laboratory of Plant Molecular Biology and Biotechnology, Department of Biology, University of North Carolina Greensboro, Greensboro, NC, USA
| | - Ayalew Ligaba-Osena
- Laboratory of Plant Molecular Biology and Biotechnology, Department of Biology, University of North Carolina Greensboro, Greensboro, NC, USA.
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9
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Deng QY, Luo JT, Zheng JM, Tan WF, Pu ZJ, Wang F. Genome-wide systematic characterization of the NRT2 gene family and its expression profile in wheat (Triticum aestivum L.) during plant growth and in response to nitrate deficiency. BMC PLANT BIOLOGY 2023; 23:353. [PMID: 37420192 DOI: 10.1186/s12870-023-04333-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 06/06/2023] [Indexed: 07/09/2023]
Abstract
BACKGROUND Wheat (Triticum aestivum L.) is a major cereal crop that is grown worldwide, and it is highly dependent on sufficient N supply. The molecular mechanisms associated with nitrate uptake and assimilation are still poorly understood in wheat. In plants, NRT2 family proteins play a crucial role in NO3- acquisition and translocation under nitrate limited conditions. However, the biological functions of these genes in wheat are still unclear, especially their roles in NO3- uptake and assimilation. RESULTS In this study, a comprehensive analysis of wheat TaNRT2 genes was conducted using bioinformatics and molecular biology methods, and 49 TaNRT2 genes were identified. A phylogenetic analysis clustered the TaNRT2 genes into three clades. The genes that clustered on the same phylogenetic branch had similar gene structures and nitrate assimilation functions. The identified genes were further mapped onto the 13 wheat chromosomes, and the results showed that a large duplication event had occurred on chromosome 6. To explore the TaNRT2 gene expression profiles in wheat, we performed transcriptome sequencing after low nitrate treatment for three days. Transcriptome analysis revealed the expression levels of all TaNRT2 genes in shoots and roots, and based on the expression profiles, three highly expressed genes (TaNRT2-6A.2, TaNRT2-6A.6, and TaNRT2-6B.4) were selected for qPCR analysis in two different wheat cultivars ('Mianmai367' and 'Nanmai660') under nitrate-limited and normal conditions. All three genes were upregulated under nitrate-limited conditions and highly expressed in the high nitrogen use efficiency (NUE) wheat 'Mianmai367' under low nitrate conditions. CONCLUSION We systematically identified 49 NRT2 genes in wheat and analysed the transcript levels of all TaNRT2s under nitrate deficient conditions and over the whole growth period. The results suggest that these genes play important roles in nitrate absorption, distribution, and accumulation. This study provides valuable information and key candidate genes for further studies on the function of TaNRT2s in wheat.
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Affiliation(s)
- Qing-Yan Deng
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, China
- Environment-Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu, 610066, Sichuan, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China (Ministry of Agriculture and Rural Affairs of P.R.C.), Chengdu, Sichuan, 610066, China
| | - Jiang-Tao Luo
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, China
- Environment-Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu, 610066, Sichuan, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China (Ministry of Agriculture and Rural Affairs of P.R.C.), Chengdu, Sichuan, 610066, China
| | - Jian-Min Zheng
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, China
- Environment-Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu, 610066, Sichuan, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China (Ministry of Agriculture and Rural Affairs of P.R.C.), Chengdu, Sichuan, 610066, China
| | - Wen-Fang Tan
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, China.
- Environment-Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu, 610066, Sichuan, China.
| | - Zong-Jun Pu
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, China.
- Environment-Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu, 610066, Sichuan, China.
- Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China (Ministry of Agriculture and Rural Affairs of P.R.C.), Chengdu, Sichuan, 610066, China.
| | - Fang Wang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, China.
- Environment-Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu, 610066, Sichuan, China.
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10
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Zafer MZ, Tahir MHN, Khan Z, Sajjad M, Gao X, Bakhtavar MA, Waheed U, Siddique M, Geng Z, Ur Rehman S. Genome-Wide Characterization and Sequence Polymorphism Analyses of Glycine max Fibrillin ( FBN) Revealed Its Role in Response to Drought Condition. Genes (Basel) 2023; 14:1188. [PMID: 37372368 DOI: 10.3390/genes14061188] [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: 04/15/2023] [Revised: 05/09/2023] [Accepted: 05/12/2023] [Indexed: 06/29/2023] Open
Abstract
The fibrillin (FBN) gene family is widely distributed in all photosynthetic organisms. Members of this gene family are involved in plant growth and development and their response to various biotic and abiotic stress factors. In this study, 16 members of FBN were identified in Glycine max and characterized by using different bioinformatics tools. Phylogenetic analysis classified FBN genes into seven groups. The presence of stress-related cis-elements in the upstream region of GmFBN highlighted their role in tolerance against abiotic stresses. To further decipher the function, physiochemical properties, conserved motifs, chromosomal localization, subcellular localization, and cis-acting regulatory elements were also analyzed. Gene expression analysis based on FPKM values revealed that GmFBNs greatly enhanced soybean drought tolerance and controlled the expression of several genes involved in drought response, except for GmFBN-4, GmFBN-5, GmFBN-6, GmFBN-7 and GmFBN-9. For high throughput genotyping, an SNP-based CAPS marker was also developed for the GmFBN-15 gene. The CAPS marker differentiated soybean genotypes based on the presence of either the GmFBN-15-G or GmFBN-15-A alleles in the CDS region. Association analysis showed that G. max accessions containing the GmFBN-15-A allele at the respective locus showed higher thousand seed weight compared to accessions containing the GmFBN-15-G allele. This research has provided the basic information to further decipher the function of FBN in soybean.
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Affiliation(s)
- Muhammad Zeshan Zafer
- SINO-PAK Joint Research Laboratory, Institute of Plant Breeding and Biotechnology, Muhammad Nawaz Shareef, University of Agriculture, Multan 66000, Pakistan
- Institute of Plant Breeding and Biotechnology, Muhammad Nawaz Shareef, University of Agriculture, Multan 66000, Pakistan
| | - Muhammad Hammad Nadeem Tahir
- Institute of Plant Breeding and Biotechnology, Muhammad Nawaz Shareef, University of Agriculture, Multan 66000, Pakistan
| | - Zulqurnain Khan
- SINO-PAK Joint Research Laboratory, Institute of Plant Breeding and Biotechnology, Muhammad Nawaz Shareef, University of Agriculture, Multan 66000, Pakistan
- Institute of Plant Breeding and Biotechnology, Muhammad Nawaz Shareef, University of Agriculture, Multan 66000, Pakistan
| | - Muhammad Sajjad
- Department of Biosciences, COMSATS University, Islamabad (CUI), Park Road, Islamabad 45550, Pakistan
| | - Xiangkuo Gao
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming 650204, China
| | - Muhammad Amir Bakhtavar
- Institute of Plant Breeding and Biotechnology, Muhammad Nawaz Shareef, University of Agriculture, Multan 66000, Pakistan
| | - Ummara Waheed
- Institute of Plant Breeding and Biotechnology, Muhammad Nawaz Shareef, University of Agriculture, Multan 66000, Pakistan
| | - Maria Siddique
- Department of Environmental Sciences, COMSATS University Islamabad, Abbottabad Campus, Abbottabad 22060, Pakistan
| | - Zhide Geng
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming 650204, China
| | - Shoaib Ur Rehman
- SINO-PAK Joint Research Laboratory, Institute of Plant Breeding and Biotechnology, Muhammad Nawaz Shareef, University of Agriculture, Multan 66000, Pakistan
- Institute of Plant Breeding and Biotechnology, Muhammad Nawaz Shareef, University of Agriculture, Multan 66000, Pakistan
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Zhang M, Zhang W, Zheng Z, Zhang Z, Hua B, Liu J, Miao M. Genome-Wide Identification and Expression Analysis of NPF Genes in Cucumber ( Cucumis sativus L.). PLANTS (BASEL, SWITZERLAND) 2023; 12:1252. [PMID: 36986940 PMCID: PMC10057324 DOI: 10.3390/plants12061252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/04/2023] [Accepted: 03/07/2023] [Indexed: 06/19/2023]
Abstract
The NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER family (NPF) proteins perform an essential role in regulating plant nitrate absorption and distribution and in improving plant nitrogen use efficiency. In this study, cucumber (Cucumis sativus L.) NPF genes were comprehensively analyzed at the whole genome level, and 54 NPF genes were found to be unevenly distributed on seven chromosomes in the cucumber genome. The phylogenetic analysis showed that these genes could be divided into eight subfamilies. We renamed all CsNPF genes according to the international nomenclature, based on their homology with AtNPF genes. By surveying the expression profiles of CsNPF genes in various tissues, we found that CsNPF6.4 was specifically expressed in roots, indicating that CsNPF6.4 may play a role in N absorption; CsNPF6.3 was highly expressed in petioles, which may be related to NO3- storage in petioles; and CsNPF2.8 was highly expressed in fruits, which may promote NO3- transport to the embryos. We further examined their expression patterns under different abiotic stress and nitrogen conditions, and found that CsNPF7.2 and CsNPF7.3 responded to salt, cold, and low nitrogen stress. Taken together, our study lays a foundation for further exploration of the molecular and physiological functions of cucumber nitrate transporters.
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Affiliation(s)
- Mengying Zhang
- College of Horticulture and Landscape, Yangzhou University, Yangzhou 225009, China
| | - Wenyan Zhang
- College of Horticulture and Landscape, Yangzhou University, Yangzhou 225009, China
| | - Zijian Zheng
- College of Horticulture and Landscape, Yangzhou University, Yangzhou 225009, China
| | - Zhiping Zhang
- College of Horticulture and Landscape, Yangzhou University, Yangzhou 225009, China
| | - Bing Hua
- College of Horticulture and Landscape, Yangzhou University, Yangzhou 225009, China
| | - Jiexia Liu
- College of Horticulture and Landscape, Yangzhou University, Yangzhou 225009, China
| | - Minmin Miao
- College of Horticulture and Landscape, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou 225009, China
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Aluko OO, Kant S, Adedire OM, Li C, Yuan G, Liu H, Wang Q. Unlocking the potentials of nitrate transporters at improving plant nitrogen use efficiency. FRONTIERS IN PLANT SCIENCE 2023; 14:1074839. [PMID: 36895876 PMCID: PMC9989036 DOI: 10.3389/fpls.2023.1074839] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 01/16/2023] [Indexed: 05/27/2023]
Abstract
Nitrate ( NO 3 - ) transporters have been identified as the primary targets involved in plant nitrogen (N) uptake, transport, assimilation, and remobilization, all of which are key determinants of nitrogen use efficiency (NUE). However, less attention has been directed toward the influence of plant nutrients and environmental cues on the expression and activities of NO 3 - transporters. To better understand how these transporters function in improving plant NUE, this review critically examined the roles of NO 3 - transporters in N uptake, transport, and distribution processes. It also described their influence on crop productivity and NUE, especially when co-expressed with other transcription factors, and discussed these transporters' functional roles in helping plants cope with adverse environmental conditions. We equally established the possible impacts of NO 3 - transporters on the uptake and utilization efficiency of other plant nutrients while suggesting possible strategic approaches to improving NUE in plants. Understanding the specificity of these determinants is crucial to achieving better N utilization efficiency in crops within a given environment.
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Affiliation(s)
- Oluwaseun Olayemi Aluko
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing, China
| | - Surya Kant
- Agriculture Victoria, Grains Innovation Park, Horsham, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | | | - Chuanzong Li
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guang Yuan
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing, China
| | - Haobao Liu
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Qian Wang
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
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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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Cheng J, Tan H, Shan M, Duan M, Ye L, Yang Y, He L, Shen H, Yang Z, Wang X. Genome-wide identification and characterization of the NPF genes provide new insight into low nitrogen tolerance in Setaria. FRONTIERS IN PLANT SCIENCE 2022; 13:1043832. [PMID: 36589108 PMCID: PMC9795848 DOI: 10.3389/fpls.2022.1043832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 11/09/2022] [Indexed: 06/17/2023]
Abstract
Introduction Nitrogen (N) is essential for plant growth and yield production and can be taken up from soil in the form of nitrate or peptides. The NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER family (NPF) genes play important roles in the uptake and transportation of these two forms of N. Methods Bioinformatic analysis was used to identify and characterize the NPF genes in Setaria. RNA-seq was employed to analyze time-series low nitrate stress response of the SiNPF genes. Yeast and Arabidopsis mutant complementation were used to test the nitrate transport ability of SiNRT1.1B1 and SiNRT1.1B2. Results We identified 92 and 88 putative NPF genes from foxtail millet (Setaria italica L.) and its wild ancestor green foxtail (Setaria viridis L.), respectively. These NPF genes were divided into eight groups according to their sequence characteristics and phylogenetic relationship, with similar intron-exon structure and motifs in the same subfamily. Twenty-six tandem duplication and 13 segmental duplication events promoted the expansion of SiNPF gene family. Interestingly, we found that the tandem duplication of the SiNRT1.1B gene might contribute to low nitrogen tolerance of foxtail millet. The gene expression atlas showed that the SiNPFs were divided into two major clusters, which were mainly expressed in root and the above ground tissues, respectively. Time series transcriptomic analysis further revealed the response of these SiNPF genes to short- and long- time low nitrate stress. To provide natural variation of gene information, we carried out a haplotype analysis of these SiNPFs and identified 2,924 SNPs and 400 InDels based on the re-sequence data of 398 foxtail millet accessions. We also predicted the three-dimensional structure of the 92 SiNPFs and found that the conserved proline 492 residues were not in the substrate binding pocket. The interactions of SiNPF proteins withNO 3 - were analyzed using molecular docking and the pockets were then identified. We found that the SiNPFs-NO 3 - binding energy ranged from -3.8 to -2.7 kcal/mol. Discussion Taken together, our study provides a comprehensive understanding of the NPF gene family in Setaria and will contribute to function dissection of these genes for crop breeding aimed at improving high nitrogen use efficiency.
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Affiliation(s)
- Jinjin Cheng
- College of Agriculture, Shanxi Agricultural University, Taigu, China
| | - Helin Tan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Meng Shan
- College of Life Sciences, Shanxi Agricultural University, Taigu, China
| | - Mengmeng Duan
- College of Life Sciences, Shanxi Agricultural University, Taigu, China
| | - Ling Ye
- College of Life Sciences, Shanxi Agricultural University, Taigu, China
| | - Yulu Yang
- College of Agriculture, Shanxi Agricultural University, Taigu, China
| | - Lu He
- College of Agriculture, Shanxi Agricultural University, Taigu, China
| | - Huimin Shen
- College of Agriculture, Shanxi Agricultural University, Taigu, China
| | - Zhirong Yang
- Department of Basic Sciences, Shanxi Agricultural University, Taigu, China
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, Shanxi Agricultural University, Taigu, China
| | - Xingchun Wang
- College of Life Sciences, Shanxi Agricultural University, Taigu, China
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, Shanxi Agricultural University, Taigu, China
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