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1.
BMC Plant Biol ; 21(1): 372, 2021 Aug 13.
Artigo em Inglês | MEDLINE | ID: mdl-34388971

RESUMO

BACKGROUND: Oilseed rape (B. napus L.) has great potential for phytoremediation of cadmium (Cd)-polluted soils due to its large plant biomass production and strong metal accumulation. Soil properties and the presence of other soluble compounds or ions, cause a heterogeneous distribution of Cd. RESULTS: The aim of our study was to reveal the differential responses of B. napus to different Cd abundances. Herein, we found that high Cd (50 µM) severely inhibited the growth of B. napus, which was not repressed by low Cd (0.50 µM) under hydroponic culture system. ICP-MS assays showed that the Cd2+ concentrations in both shoots and roots under 50 µM Cd were over 10 times higher than those under 0.50 µM Cd. Under low Cd, the concentrations of only shoot Ca2+/Mn2+ and root Mn2+ were obviously changed (both reduced); under high Cd, the concentrations of most cations assayed were significantly altered in both shoots and roots except root Ca2+ and Mg2+. High-throughput transcriptomic profiling revealed a total of 18,021 and 1408 differentially expressed genes under high Cd and low Cd conditions, respectively. The biological categories related to the biosynthesis of plant cell wall components and response to external stimulus were over-accumulated under low Cd, whereas the terms involving photosynthesis, nitrogen transport and response, and cellular metal ion homeostasis were highly enriched under high Cd. Differential expression of the transporters responsible for Cd uptake (NRAMPs), transport (IRTs and ZIPs), sequestration (HMAs, ABCs, and CAXs), and detoxification (MTPs, PCR, MTs, and PCSs), and some other essential nutrient transporters were investigated, and gene co-expression network analysis revealed the core members of these Cd transporters. Some Cd transporter genes, especially NRAMPs and IRTs, showed opposite responsive patterns between high Cd and low Cd conditions. CONCLUSIONS: Our findings would enrich our understanding of the interaction between essential nutrients and Cd, and might also provide suitable gene resources and important implications for the genetic improvement of plant Cd accumulation and resistance through molecular engineering of these core genes under varying Cd abundances in soils.


Assuntos
Brassica napus/genética , Brassica napus/metabolismo , Cádmio/metabolismo , Transporte Biológico , Brassica napus/crescimento & desenvolvimento , Quelantes/metabolismo , Regulação da Expressão Gênica de Plantas , Genes de Plantas , Íons/metabolismo , Solo/química , Tetraploidia , Transcriptoma
2.
Mol Biol Rep ; 48(8): 5977-5992, 2021 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-34327662

RESUMO

BACKGROUND: Nitrogen (N) is an essential macronutrient to maintain plant growth and development. Plants absorb nitrate-N or ammonium-N in the environment and undergo reduction reactions catalyzed by nitrate reductase (NR), nitrite reductase (NIR), glutamine synthetase (GS), and glutamine oxoglutarate aminotransferase (GOGAT) within plants. METHODS AND RESULTS: A total of 42 N assimilation-related genes (NAG) members were identified in rapeseed. Darwin's evolutionary pressure analysis showed that rapeseed NAGs underwent purification selection. Cis-element analysis revealed differences in the transcriptional regulation of NAGs between Arabidopsis and rapeseed. Expression analyses revealed that NRs were expressed mainly in old leaves, NIRs were expressed mainly in old leaves and lower stem peels, while the expression situation between different subfamilies of GSs and GOGATs was more complicated. CONCLUSIONS: Differential expression of NAGs suggested that they might be involved in abiotic stresses. The above results greatly enriched our understanding of NAGs' molecular characteristics and provided central gene resources for NAGs-mediated NUE improvement in rapeseed.

3.
BMC Plant Biol ; 21(1): 288, 2021 Jun 24.
Artigo em Inglês | MEDLINE | ID: mdl-34167468

RESUMO

BACKGROUND: B-box (BBX) genes play important roles in plant growth regulation and responses to abiotic stresses. The plant growth and yield production of allotetraploid rapeseed is usually hindered by diverse nutrient stresses. However, no systematic analysis of Brassicaceae BBXs and the roles of BBXs in the regulation of nutrient stress responses have not been identified and characterized previously. RESULTS: In this study, a total of 536 BBXs were identified from nine brassicaceae species, including 32 AtBBXs, 66 BnaBBXs, 41 BoBBXs, 43 BrBBXs, 26 CrBBXs, 81 CsBBXs, 52 BnBBXs, 93 BjBBXs, and 102 BcBBXs. Syntenic analysis showed that great differences in the gene number of Brassicaceae BBXs might be caused by genome duplication. The BBXs were respectively divided into five subclasses according to their phylogenetic relationships and conserved domains, indicating their diversified functions. Promoter cis-element analysis showed that BBXs probably participated in diverse stress responses. Protein-protein interactions between BnaBBXs indicated their functions in flower induction. The expression profiles of BnaBBXs were investigated in rapeseed plants under boron deficiency, boron toxicity, nitrate limitation, phosphate shortage, potassium starvation, ammonium excess, cadmium toxicity, and salt stress conditions using RNA-seq data. The results showed that different BnaBBXs showed differential transcriptional responses to nutrient stresses, and some of them were simultaneously responsive to diverse nutrient stresses. CONCLUSIONS: Taken together, the findings investigated in this study provided rich resources for studying Brassicaceae BBX gene family and enriched potential clues in the genetic improvement of crop stress resistance.


Assuntos
Brassica napus/genética , Brassicaceae/genética , Genes de Plantas/genética , Fatores de Transcrição/genética , Brassica napus/fisiologia , Sequência Conservada , Regulação da Expressão Gênica de Plantas/genética , Genes de Plantas/fisiologia , Estudo de Associação Genômica Ampla , Filogenia , Mapas de Interação de Proteínas , Estresse Fisiológico , Sintenia , Tetraploidia , Fatores de Transcrição/fisiologia
4.
J Exp Bot ; 72(15): 5687-5708, 2021 07 28.
Artigo em Inglês | MEDLINE | ID: mdl-33989425

RESUMO

The large size and complexity of the allotetraploid rapeseed (Brassica napus) genome present huge challenges for understanding salinity resistance in this important crop. In this study, we identified two rapeseed genotypes with significantly different degrees of salinity resistance and examined the underlying mechanisms using an integrated analysis of phenomics, ionomics, genomics, and transcriptomics. Under salinity, a higher accumulation of osmoregulation substances and better root-system architecture was observed in the resistant genotype, H159, than in the sensitive one, L339. A lower shoot Na+ concentration and a higher root vacuolar Na+ concentration indicated lower root-to-shoot translocation and higher compartmentation in H159 than in L339. Whole-genome re-sequencing (WGRS) and transcriptome sequencing identified numerous DNA variants and differentially expressed genes involved in abiotic stress responses and ion transport. Combining ionomics with transcriptomics identified plasma membrane-localized BnaC2.HKT1;1 and tonoplast-localized BnaC5.NHX2 as the central factors regulating differential root xylem unloading and vacuolar sequestration of Na+ between the two genotypes. Identification of polymorphisms by WGRS and PCR revealed two polymorphic MYB-binding sites in the promoter regions that might determine the differential gene expression of BnaC2.HKT1;1 and BnaC5.NHX2. Our multiomics approach thus identified core transporters involved in Na+ translocation and compartmentation that regulate salinity resistance in rapeseed. Our results may provide elite gene resources for the improvement of salinity resistance in this crop, and our multiomics approach can be applied to other similar studies.


Assuntos
Brassica napus , Brassica napus/genética , Brassica napus/metabolismo , Regulação da Expressão Gênica de Plantas , Salinidade , Sódio/metabolismo , Estresse Fisiológico
5.
BMC Plant Biol ; 20(1): 534, 2020 Nov 24.
Artigo em Inglês | MEDLINE | ID: mdl-33228523

RESUMO

BACKGROUND: Salinity severely inhibit crop growth, yield, and quality worldwide. Allotetraploid rapeseed (Brassica napus L.), a major glycophyte oil crop, is susceptible to salinity. Understanding the physiological and molecular strategies of rapeseed salinity resistance is a promising and cost-effective strategy for developing highly resistant cultivars. RESULTS: First, early leaf senescence was identified and root system growth was inhibited in rapeseed plants under severe salinity conditions. Electron microscopic analysis revealed that 200 mM NaCl induced fewer leaf trichomes and stoma, cell plasmolysis, and chloroplast degradation. Primary and secondary metabolite assays showed that salinity led to an obviously increased anthocyanin, osmoregulatory substances, abscisic acid, jasmonic acid, pectin, cellulose, reactive oxygen species, and antioxidant activity, and resulted in markedly decreased photosynthetic pigments, indoleacetic acid, cytokinin, gibberellin, and lignin. ICP-MS assisted ionomics showed that salinity significantly constrained the absorption of essential elements, including the nitrogen, phosphorus, potassium, calcium, magnesium, iron, mangnese, copper, zinc, and boron nutrients, and induced the increase in the sodium/potassium ratio. Genome-wide transcriptomics revealed that the differentially expressed genes were involved mainly in photosynthesis, stimulus response, hormone signal biosynthesis/transduction, and nutrient transport under salinity. CONCLUSIONS: The high-resolution salt-responsive gene expression profiling helped the efficient characterization of central members regulating plant salinity resistance. These findings might enhance integrated comprehensive understanding of the morpho-physiologic and molecular responses to salinity and provide elite genetic resources for the genetic modification of salinity-resistant crop species.


Assuntos
Brassica napus/genética , Fotossíntese/efeitos dos fármacos , Reguladores de Crescimento de Plantas/metabolismo , Transcriptoma/efeitos dos fármacos , Brassica napus/efeitos dos fármacos , Brassica napus/fisiologia , Perfilação da Expressão Gênica , Homeostase/efeitos dos fármacos , Íons/metabolismo , Nitrogênio/metabolismo , Folhas de Planta/efeitos dos fármacos , Folhas de Planta/genética , Folhas de Planta/fisiologia , Estômatos de Plantas/efeitos dos fármacos , Estômatos de Plantas/genética , Estômatos de Plantas/fisiologia , Salinidade , Cloreto de Sódio/farmacologia , Tricomas/efeitos dos fármacos , Tricomas/genética , Tricomas/fisiologia
6.
Int J Mol Sci ; 21(22)2020 Nov 10.
Artigo em Inglês | MEDLINE | ID: mdl-33182819

RESUMO

Improving crop nitrogen (N) limitation adaptation (NLA) is a core approach to enhance N use efficiency (NUE) and reduce N fertilizer application. Rapeseed has a high demand for N nutrients for optimal plant growth and seed production, but it exhibits low NUE. Epigenetic modification, such as DNA methylation and modification from small RNAs, is key to plant adaptive responses to various stresses. However, epigenetic regulatory mechanisms underlying NLA and NUE remain elusive in allotetraploid B. napus. In this study, we identified overaccumulated carbohydrate, and improved primary and lateral roots in rapeseed plants under N limitation, which resulted in decreased plant nitrate concentrations, enhanced root-to-shoot N translocation, and increased NUE. Transcriptomics and RT-qPCR assays revealed that N limitation induced the expression of NRT1.1, NRT1.5, NRT1.7, NRT2.1/NAR2.1, and Gln1;1, and repressed the transcriptional levels of CLCa, NRT1.8, and NIA1. High-resolution whole genome bisulfite sequencing characterized 5094 differentially methylated genes involving ubiquitin-mediated proteolysis, N recycling, and phytohormone metabolism under N limitation. Hypermethylation/hypomethylation in promoter regions or gene bodies of some key N-metabolism genes might be involved in their transcriptional regulation by N limitation. Genome-wide miRNA sequencing identified 224 N limitation-responsive differentially expressed miRNAs regulating leaf development, amino acid metabolism, and plant hormone signal transduction. Furthermore, degradome sequencing and RT-qPCR assays revealed the miR827-NLA pathway regulating limited N-induced leaf senescence as well as the miR171-SCL6 and miR160-ARF17 pathways regulating root growth under N deficiency. Our study provides a comprehensive insight into the epigenetic regulatory mechanisms underlying rapeseed NLA, and it will be helpful for genetic engineering of NUE in crop species through epigenetic modification of some N metabolism-associated genes.


Assuntos
Brassica napus/genética , Brassica napus/metabolismo , Epigênese Genética , Nitrogênio/metabolismo , Adaptação Fisiológica , Brassica napus/crescimento & desenvolvimento , Metilação de DNA , Fertilizantes , Perfilação da Expressão Gênica , Regulação da Expressão Gênica de Plantas , Genoma de Planta , MicroRNAs/genética , MicroRNAs/metabolismo , Modelos Biológicos , RNA de Plantas/genética , RNA de Plantas/metabolismo , Tetraploidia
7.
Int J Mol Sci ; 21(10)2020 May 12.
Artigo em Inglês | MEDLINE | ID: mdl-32408717

RESUMO

Soil salinity is a main abiotic stress in agriculture worldwide. The Na+/H+ antiporters (NHXs) play pivotal roles in intracellular Na+ excretion and vacuolar Na+ compartmentalization, which are important for plant salt stress resistance (SSR). However, few systematic analyses of NHXs has been reported in allotetraploid rapeseed so far. Here, a total of 18 full-length NHX homologs, representing seven subgroups (NHX1-NHX8 without NHX5), were identified in the rapeseed genome (AnAnCnCn). Number variations of BnaNHXs might indicate their significantly differential roles in the regulation of rapeseed SSR. BnaNHXs were phylogenetically divided into three evolutionary clades, and the members in the same subgroups had similar physiochemical characteristics, gene/protein structures, and conserved Na+ transport motifs. Darwin´s evolutionary pressure analysis suggested that BnaNHXs suffered from strong purifying selection. The cis-element analysis revealed the differential transcriptional regulation of NHXs between the model Arabidopsis and B. napus. Differential expression of BnaNHXs under salt stress, different nitrogen forms (ammonium and nitrate), and low phosphate indicated their potential involvement in the regulation of rapeseed SSR. Global landscapes of BnaNHXs will give an integrated understanding of their family evolution and molecular features, which will provide elite gene resources for the genetic improvement of plant SSR through regulating the NHX-mediated Na+ transport.


Assuntos
Brassica napus/genética , Resistência a Medicamentos/genética , Família Multigênica , Proteínas de Plantas/genética , Estresse Salino/genética , Trocadores de Sódio-Hidrogênio/genética , Arabidopsis/genética , Arabidopsis/metabolismo , Brassica napus/classificação , Brassica napus/metabolismo , Perfilação da Expressão Gênica/métodos , Regulação da Expressão Gênica de Plantas , Genoma de Planta/genética , Filogenia , Proteínas de Plantas/metabolismo , Salinidade , Seleção Genética , Sódio/metabolismo , Trocadores de Sódio-Hidrogênio/metabolismo , Estresse Fisiológico/genética
8.
Int J Mol Sci ; 21(6)2020 Mar 21.
Artigo em Inglês | MEDLINE | ID: mdl-32245240

RESUMO

Nitrogen (N) is essential for plant growth and crop productivity. Organic N is a major form of remobilized N in plants' response to N limitation. It is necessary to understand the regulatory role of N limitation adaption (NLA) in organic N remobilization for this adaptive response. Transcriptional and proteomic analyses were integrated to investigate differential responses of wild-type (WT) and nla mutant plants to N limitation and to identify the core organic N transporters targeted by NLA. Under N limitation, the nla mutant presented an early senescence with faster chlorophyll loss and less anthocyanin accumulation than the WT, and more N was transported out of the aging leaves in the form of amino acids. High-throughput transcriptomic and proteomic analyses revealed that N limitation repressed genes involved in photosynthesis and protein synthesis, and promoted proteolysis; these changes were higher in the nla mutant than in the WT. Both transcriptional and proteomic profiling demonstrated that LHT1, responsible for amino acid remobilization, were only significantly upregulated in the nla mutant under N limitation. These findings indicate that NLA might target LHT1 and regulate organic N remobilization, thereby improving our understanding of the regulatory role of NLA on N remobilization under N limitation.


Assuntos
Sistemas de Transporte de Aminoácidos Básicos/metabolismo , Sistemas de Transporte de Aminoácidos/metabolismo , Proteínas de Arabidopsis/metabolismo , Arabidopsis/metabolismo , Nitrogênio/metabolismo , Ubiquitina-Proteína Ligases/metabolismo , Adaptação Fisiológica/genética , Envelhecimento/metabolismo , Envelhecimento/fisiologia , Sistemas de Transporte de Aminoácidos/genética , Sistemas de Transporte de Aminoácidos Básicos/genética , Antocianinas/genética , Antocianinas/metabolismo , Arabidopsis/genética , Proteínas de Arabidopsis/genética , Senescência Celular/genética , Clorofila/metabolismo , Cromatografia Líquida , Perfilação da Expressão Gênica , Regulação da Expressão Gênica de Plantas/genética , Ontologia Genética , Fotossíntese/genética , Folhas de Planta/metabolismo , Biossíntese de Proteínas/genética , Proteólise , Proteômica , Espectrometria de Massas em Tandem , Ubiquitina-Proteína Ligases/genética
9.
BMC Plant Biol ; 20(1): 151, 2020 Apr 08.
Artigo em Inglês | MEDLINE | ID: mdl-32268885

RESUMO

BACKGROUND: Nitrogen (N), referred to as a "life element", is a macronutrient essential for optimal plant growth and yield production. Amino acid (AA) permease (AAP) genes play pivotal roles in root import, long-distance translocation, remobilization of organic amide-N from source organs to sinks, and other environmental stress responses. However, few systematic analyses of AAPs have been reported in Brassica napus so far. RESULTS: In this study, we identified a total of 34 full-length AAP genes representing eight subgroups (AAP1-8) from the allotetraploid rapeseed genome (AnAnCnCn, 2n = 4x = 38). Great differences in the homolog number among the BnaAAP subgroups might indicate their significant differential roles in the growth and development of rapeseed plants. The BnaAAPs were phylogenetically divided into three evolutionary clades, and the members in the same subgroups had similar physiochemical characteristics, gene/protein structures, and conserved AA transport motifs. Darwin's evolutionary analysis suggested that BnaAAPs were subjected to strong purifying selection pressure. Cis-element analysis showed potential differential transcriptional regulation of AAPs between the model Arabidopsis and B. napus. Differential expression of BnaAAPs under nitrate limitation, ammonium excess, phosphate shortage, boron deficiency, cadmium toxicity, and salt stress conditions indicated their potential involvement in diverse nutrient stress responses. CONCLUSIONS: The genome-wide identification of BnaAAPs will provide a comprehensive insight into their family evolution and AAP-mediated AA transport under diverse abiotic stresses. The molecular characterization of core AAPs can provide elite gene resources and contribute to the genetic improvement of crop stress resistance through the modulation of AA transport.


Assuntos
Sistemas de Transporte de Aminoácidos/genética , Brassica napus/enzimologia , Regulação da Expressão Gênica de Plantas , Estresse Fisiológico , Sistemas de Transporte de Aminoácidos/metabolismo , Brassica napus/genética , Estudo de Associação Genômica Ampla , Filogenia
10.
J Exp Bot ; 70(19): 5437-5455, 2019 10 15.
Artigo em Inglês | MEDLINE | ID: mdl-31232451

RESUMO

Oilseed rape (Brassica napus) has great potential for phytoremediation of cadmium (Cd)-polluted soils due to its large plant biomass production and strong metal accumulation. Enhanced plant Cd resistance (PCR) is a crucial prerequisite for phytoremediation through hyper-accumulation of excess Cd. However, the complexity of the allotetraploid genome of rapeseed hinders our understanding of PCR. To explore rapeseed Cd-resistance mechanisms, we examined two genotypes, 'ZS11' (Cd-resistant) and 'W10' (Cd-sensitive), that exhibit contrasting PCR while having similar tissue Cd concentrations, and characterized their different fingerprints in terms of plant morphophysiology (electron microscopy), ion abundance (inductively coupled plasma mass spectrometry), DNA variation (whole-genome resequencing), transcriptomics (high-throughput mRNA sequencing), and metabolomics (ultra-high performance liquid chromatography-mass spectrometry). Fine isolation of cell components combined with ionomics revealed that more Cd accumulated in the shoot vacuoles and root pectins of the resistant genotype than in the sensitive one. Genome and transcriptome sequencing identified numerous DNA variants and differentially expressed genes involved in pectin modification, ion binding, and compartmentalization. Transcriptomics-assisted gene co-expression networks characterized BnaCn.ABCC3 and BnaA8.PME3 as the central members involved in the determination of rapeseed PCR. High-resolution metabolic profiles revealed greater accumulation of shoot Cd chelates, and stronger biosynthesis and higher demethylation of root pectins in the resistant genotype than in the sensitive one. Our comprehensive examination using a multiomics approach has greatly improved our understanding of the role of subcellular reallocation of Cd in the determination of PCR.


Assuntos
Brassica napus/genética , Brassica napus/metabolismo , Cádmio/metabolismo , Genoma de Planta , Poluentes do Solo/metabolismo , Biodegradação Ambiental , Cádmio/toxicidade , Metaboloma , Poluentes do Solo/toxicidade , Transcriptoma
11.
PLoS One ; 13(12): e0208648, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-30571734

RESUMO

The Chloride Channel (CLC) gene family is reported to be involved in vacuolar nitrate (NO3-) transport. Nitrate distribution to the cytoplasm is beneficial for enhancing NO3- assimilation and plays an important role in the regulation of nitrogen (N) use efficiency (NUE). In this study, genomic information, high-throughput transcriptional profiles, and gene co-expression analysis were integrated to identify the CLCs (BnaCLCs) in Brassica napus. The decreased NO3- concentration in the clca-2 mutant up-regulated the activities of nitrate reductase and glutamine synthetase, contributing to increase N assimilation and higher NUE in Arabidopsis thaliana. The genome-wide identification of 22BnaCLC genes experienced strong purifying selection. Segmental duplication was the major driving force in the expansion of the BnaCLC gene family. The most abundant cis-acting regulatory elements in the gene promoters, including DNA-binding One Zinc Finger, W-box, MYB, and GATA-box, might be involved in the transcriptional regulation of BnaCLCs expression. High-throughput transcriptional profiles and quantitative real-time PCR results showed that BnaCLCs responded differentially to distinct NO3- regimes. Transcriptomics-assisted gene co-expression network analysis identified BnaA7.CLCa-3 as the core member of the BnaCLC family, and this gene might play a central role in vacuolar NO3- transport in crops. The BnaCLC members also showed distinct expression patterns under phosphate depletion and cadmium toxicity. Taken together, our results provide comprehensive insights into the vacuolar BnaCLCs and establish baseline information for future studies on BnaCLCs-mediated vacuolar NO3- storage and its effect on NUE.


Assuntos
Proteínas de Transporte de Ânions/genética , Brassica rapa/genética , Canais de Cloreto/genética , Proteínas de Plantas/genética , Estresse Fisiológico/genética , Vacúolos/genética , Proteínas de Transporte de Ânions/metabolismo , Arabidopsis/genética , Arabidopsis/metabolismo , Brassica rapa/metabolismo , Cádmio/metabolismo , Canais de Cloreto/metabolismo , Sequência Conservada , Produtos Agrícolas/genética , Produtos Agrícolas/metabolismo , Regulação da Expressão Gênica de Plantas , Glutamato-Amônia Ligase/metabolismo , Nitrato Redutase/metabolismo , Nitratos/metabolismo , Nitrogênio/metabolismo , Fosfatos/metabolismo , Filogenia , Melhoramento Vegetal , Proteínas de Plantas/metabolismo , Regiões Promotoras Genéticas , Estresse Fisiológico/fisiologia , Transcrição Genética , Vacúolos/metabolismo
12.
BMC Plant Biol ; 18(1): 322, 2018 Dec 04.
Artigo em Inglês | MEDLINE | ID: mdl-30509163

RESUMO

BACKGROUND: Nitrogen (N) is a macronutrient that is essential for optimal plant growth and seed yield. Allotetraploid rapeseed (AnAnCnCn, 2n = 4x = 38) has a higher requirement for N fertilizers whereas exhibiting a lower N use efficiency (NUE) than cereal crops. N limitation adaptation (NLA) is pivotal for enhancing crop NUE and reducing N fertilizer use in yield production. Therefore, revealing the genetic and molecular mechanisms underlying NLA is urgent for the genetic improvement of NUE in rapeseed and other crop species with complex genomes. RESULTS: In this study, we integrated physiologic, genomic and transcriptomic analyses to comprehensively characterize the adaptive strategies of oilseed rape to N limitation stresses. Under N limitations, we detected accumulated anthocyanin, reduced nitrate (NO3-) and total N concentrations, and enhanced glutamine synthetase activity in the N-starved rapeseed plants. High-throughput transcriptomics revealed that the pathways associated with N metabolism and carbon fixation were highly over-represented. The expression of the genes that were involved in efficient N uptake, translocation, remobilization and assimilation was significantly altered. Genome-wide identification and molecular characterization of the microR827-NLA1-NRT1.7 regulatory circuit indicated the crucial role of the ubiquitin-mediated post-translational pathway in the regulation of rapeseed NLA. Transcriptional analysis of the module genes revealed their significant functional divergence in response to N limitations between allotetraploid rapeseed and the model Arabidopsis. Association analysis in a rapeseed panel comprising 102 genotypes revealed that BnaC5.NLA1 expression was closely correlated with the rapeseed low-N tolerance. CONCLUSIONS: We identified the physiologic and genome-wide transcriptional responses of oilseed rape to N limitation stresses, and characterized the global members of the BnamiR827-BnaNLA1s-BnaNRT1.7s regulatory circuit. The transcriptomics-assisted gene co-expression network analysis accelerates the rapid identification of central members within large gene families of plant species with complex genomes. These findings would enhance our comprehensive understanding of the physiologic responses, genomic adaptation and transcriptomic alterations of oilseed rape to N limitations and provide central gene resources for the genetic improvement of crop NLA and NUE.


Assuntos
Brassica rapa/metabolismo , Nitrogênio/deficiência , Adaptação Fisiológica , Antocianinas/metabolismo , Brassica rapa/genética , Brassica rapa/fisiologia , Regulação da Expressão Gênica de Plantas , Glutamato-Amônia Ligase/metabolismo , Nitratos/metabolismo , Nitrogênio/metabolismo , Tetraploidia
13.
G3 (Bethesda) ; 8(8): 2757-2771, 2018 07 31.
Artigo em Inglês | MEDLINE | ID: mdl-29967053

RESUMO

Nitrogen (N) is a non-mineral macronutrient essential for plant growth and development. Oilseed rape (AnAnCnCn, 2n = 4x = 38) has a high requirement for N nutrients whereas showing the lowest N use efficiency (NUE) among crops. The mechanisms underlying NUE regulation in Brassica napus remain unclear because of genome complexity. In this study, we performed high-depth and -coverage whole-genome re-sequencing (WGS) of an N-efficient (higher NUE) genotype "XY15" and an N-inefficient (lower NUE) genotype "814" of rapeseed. More than 687 million 150-bp paired-end reads were generated, which provided about 93% coverage and 50× depth of the rapeseed genome. Applying stringent parameters, we identified a total of 1,449,157 single-nucleotide polymorphisms (SNPs), 335,228 InDels, 175,602 structure variations (SVs) and 86,280 copy number variations (CNVs) between the N-efficient and -inefficient genotypes. The largest proportion of various DNA polymorphisms occurred in the inter-genic regions. Unlike CNVs, the SNP/InDel and SV polymorphisms showed variation bias of the An and Cn subgenomes, respectively. Gene ontology analysis showed the genetic variants were mapped onto the genes involving N compound transport and ATPase complex metabolism, but not including N assimilation-related genes. On basis of identification of N-starvation responsive genes through high-throughput expression profiling, we also mapped these variants onto some key NUE-regulating genes, and validated their significantly differential expression between the N-efficient and -inefficient genotypes through qRT-PCR assays. Our data provide genome-wide high resolution DNA variants underlying NUE divergence in allotetraploid rapeseed genotypes, which would expedite the effective identification and functional validation of key NUE-regulating genes through genomics-assisted improvement of crop nutrient efficiency.


Assuntos
Brassica rapa/genética , Genoma de Planta , Nitrogênio/metabolismo , Polimorfismo Genético , Tetraploidia , Brassica rapa/metabolismo , Genótipo
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