scholarly journals Chickpea shows genotype-specific nodulation responses across soil nitrogen environment and root disease resistance categories

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Krista L. Plett ◽  
Sean L. Bithell ◽  
Adrian Dando ◽  
Jonathan M. Plett
Keyword(s):  
Nitrogen Fixation ◽  
Disease Resistance ◽  
Soil Nitrogen ◽  
Cellular Localization ◽  
Expression Patterns ◽  
Nodule Development ◽  
Nodule Formation ◽  
Symbiotic Relationship ◽  
Plant Genotype ◽  
Factors Affecting

Abstract Background The ability of chickpea to obtain sufficient nitrogen via its symbiotic relationship with Mesorhizobium ciceri is of critical importance in supporting growth and grain production. A number of factors can affect this symbiotic relationship including abiotic conditions, plant genotype, and disruptions to host signalling/perception networks. In order to support improved nodule formation in chickpea, we investigated how plant genotype and soil nutrient availability affect chickpea nodule formation and nitrogen fixation. Further, using transcriptomic profiling, we sought to identify gene expression patterns that characterize highly nodulated genotypes. Results A study involving six chickpea varieties demonstrated large genotype by soil nitrogen interaction effects on nodulation and further identified agronomic traits of genotypes (such as shoot weight) associated with high nodulation. We broadened our scope to consider 29 varieties and breeding lines to examine the relationship between soilborne disease resistance and the number of nodules developed and real-time nitrogen fixation. Results of this larger study supported the earlier genotype specific findings, however, disease resistance did not explain differences in nodulation across genotypes. Transcriptional profiling of six chickpea genotypes indicates that genes associated with signalling, N transport and cellular localization, as opposed to genes associated with the classical nodulation pathway, are more likely to predict whether a given genotype will exhibit high levels of nodule formation. Conclusions This research identified a number of key abiotic and genetic factors affecting chickpea nodule development and nitrogen fixation. These findings indicate that an improved understanding of genotype-specific factors affecting chickpea nodule induction and function are key research areas necessary to improving the benefits of rhizobial symbiosis in chickpea.

scholarly journals Induction and Spatial Organization of Polyamine Biosynthesis During Nodule Development in Lotus japonicus

2004 ◽  
Vol 17 (12) ◽  
pp. 1283-1293 ◽  
Author(s):  
Emmanouil Flemetakis ◽  
Rodica C. Efrose ◽  
Guilhem Desbrosses ◽  
Maria Dimou ◽  
Costas Delis ◽  
...  
Keyword(s):  
Nitrogen Fixation ◽  
Symbiotic Nitrogen Fixation ◽  
Expression Patterns ◽  
Lotus Japonicus ◽  
Cyclin D3 ◽  
Nodule Development ◽  
Cdna Clones ◽  
Long Distance ◽  
Polyamine Biosynthesis ◽  
Transcript Levels

Putrescine and other polyamines are produced by two alternative pathways in plants. One pathway starts with the enzyme arginine decarboxylase (ADC; EC 4.1.1.19), the other with ornithine decarboxylase (ODC; EC 4.1.1.17). Metabolite profiling of nitrogen-fixing Lotus japonicus nodules, using gas chromatography coupled to mass spectrometry, revealed a two- to sixfold increase in putrescine levels in mature nodules compared with other organs. Genes involved in polyamine biosynthesis in L. japonicus nodules were identified by isolating cDNA clones encoding ADC (LjADC1) and ODC (LjODC) from a nodule library. Searches of the public expressed sequence tag databases revealed the presence of a second gene encoding ADC (LjADC2). Real-time reverse-transcription-polymerase chain reaction analysis showed that LjADC1 and LjADC2 were expressed throughout the plant, while LjODC transcripts were detected only in nodules and roots. Induction of LjODC and LjADC gene expression during nodule development preceded symbiotic nitrogen fixation. Transcripts accumulation was maximal at 10 days postinfection, when a 6.5-fold increase in the transcript levels of LjODC was observed in comparison with the uninfected roots, while a twofold increase in the transcript levels of LjADC1 and LjADC2 was detected. At later stages of nodule development, transcripts for ADC drastically declined, while in the case of ODC, transcript accumulation was higher than that in roots until after 21 days postinfection. The expression profile of genes involved in putrescine biosynthesis correlated well with the expression patterns of genes involved in cell division and expansion, including a L. japonicus Cyclin D3 and an α-expansin gene. Spatial localization of LjODC and LjADC1 gene transcripts in developing nodules revealed that both transcripts were expressed in nodule inner cortical cells and in the central tissue. High levels of LjADC1 transcripts were also observed in both nodule and connecting root vascular tissue, suggesting that putrescine and other polyamines may be subject to long-distance transport. Our results indicate that polyamines are primarily involved in physiological and cellular processes involved in nodule development, rather than in processes that support directly symbiotic nitrogen fixation and assimilation.

scholarly journals Excess nitrate induces nodule greening and reduces transcript and protein expression levels of soybean leghaemoglobins

2020 ◽  
Vol 126 (1) ◽  
pp. 61-72
Author(s):  
Mengke Du ◽  
Zhi Gao ◽  
Xinxin Li ◽  
Hong Liao
Keyword(s):  
Nitrogenase Activity ◽  
Expression Patterns ◽  
Bioinformatic Analysis ◽  
Nodule Development ◽  
Nodule Formation ◽  
N Availability ◽  
Soybean Plants ◽  
Systematic Identification ◽  
Biological Nitrogen ◽  
Soybean Nodulation

Abstract Background and Aims Efficient biological nitrogen fixation (BNF) requires leghaemoglobin (Lb) to modulate oxygen pressure in nodules. Excess N supply severely inhibits BNF through effects on Lb during nodulation. As yet, a systematic identification and characterization of Lb-encoding genes in soybean has not been reported. Methods The effects of N on BNF were studied in soybean plants inoculated with rhizobia and exposed to excess or low N availability in hydroponic cultures. To identify soybean Lb proteins, BLAST searches were performed on the Phytozome website. Bioinformatic analysis of identified GmLbs was then carried out to investigate gene structure, protein homology and phylogenetic relationships. Finally, quantitative real-time PCR was employed to analyse the expression patterns of soybean Lb genes in various tissues and in response to high N availability. Key Results Excess N significantly accelerated nodule senescence and the production of green Lb in nodules. In total, seven haemoglobin (Hb) genes were identified from the soybean genome, with these Hb genes readily split into two distinct clades containing predominantly symbiosis-associated or non-symbiotic Hb members. Expression analysis revealed that all of the symbiosis-associated Lbs except GmLb5 were specifically expressed in nodules, while the non-symbiotic GmHbs, GmHb1 and GmHb2, were predominantly expressed in leaves and roots, respectively. Among identified GmLbs, GmLb1–4 are the major Lb genes acting in soybean nodulation, and each one is also significantly suppressed by exposure to excess N. Conclusions Taken together, the results show that excess N inhibits BNF by reducing nodule formation, Lb concentration and nitrogenase activity. The characteristics of the entire Hb family were analysed, and we found that GmLb1–4 are closely associated with nodule development and N2 fixation. This works forms the basis for further investigations of the role of Lbs in soybean nodulation.

scholarly journals Transcription Profiling of Soybean Nodulation by Bradyrhizobium japonicum

2008 ◽  
Vol 21 (5) ◽  
pp. 631-645 ◽  
Author(s):  
Laurent Brechenmacher ◽  
Moon-Young Kim ◽  
Marisol Benitez ◽  
Min Li ◽  
Trupti Joshi ◽  
...  
Keyword(s):  
Nitrogen Fixation ◽  
Bradyrhizobium Japonicum ◽  
Root Nodules ◽  
Expression Patterns ◽  
Root Hairs ◽  
Defense Responses ◽  
Nodule Development ◽  
Plant Defense Responses ◽  
Polymerase Chain ◽  
High Level

Legumes interact with nodulating bacteria that convert atmospheric nitrogen into ammonia for plant use. This nitrogen fixation takes place within root nodules that form after infection of root hairs by compatible rhizobia. Using cDNA microarrays, we monitored gene expression in soybean (Glycine max) inoculated with the nodulating bacterium Bradyrhizobium japonicum 4, 8, and 16 days after inoculation, timepoints that coincide with nodule development and the onset of nitrogen fixation. This experiment identified several thousand genes that were differentially expressed in response to B. japonicum inoculation. Expression of 27 genes was analyzed by quantitative reverse transcriptase-polymerase chain reaction, and their expression patterns mimicked the microarray results, confirming integrity of analyses. The microarray results suggest that B. japonicum reduces plant defense responses during nodule development. In addition, the data revealed a high level of regulatory complexity (transcriptional, post-transcriptional, translational, post-translational) that is likely essential for development of the symbiosis and adjustment to an altered nutritional status.

scholarly journals A Convenient, Soil-Free Method for the Production of Root Nodules in Soybean to Study the Effects of Exogenous Additives

2018 ◽  
Author(s):  
Swarup Roy Choudhury ◽  
Sarah M. Johns ◽  
Sona Pandey
Keyword(s):  
Nitrogen Fixation ◽  
Biological Nitrogen Fixation ◽  
Root Nodules ◽  
Growth Conditions ◽  
Nodule Development ◽  
Nodule Formation ◽  
Legume Crop ◽  
Simple Protocol ◽  
Biological Nitrogen

Legumes develop root nodules that harbour endosymbiotic bacteria, rhizobia. These rhizobia convert nitrogen to ammonia by biological nitrogen fixation. A thorough understanding of the biological nitrogen fixation in legumes and its regulation is key to develop sustainable agriculture. It is well known that plant hormones affect nodule formation; however, most studies are limited to model legumes due to their suitability for in vitro, plate-based assays. Specifically, it is almost impossible to measure the effects of exogenous hormones or other additives during nodule development in crop legumes such as soybean as they have huge root system in soil. To circumvent this issue, the present research develops suitable media and growth conditions for efficient nodule development under in vitro, soil free conditions in an important legume crop, soybean. Moreover, we also evaluate the effects of all major phytohormones during soybean nodulation under identical conditions. This versatile, inexpensive, scalable and simple protocol provides several advantages over previously established methods. It is extremely time-and resource-efficient, does not require special training or equipment, and produces highly reproducible results. The approach is expandable to other large legumes as well as for other exogenous additives.

scholarly journals Nitrate inhibits nodule organogenesis through inhibition of cytokinin biosynthesis in Lotus japonicus

2020 ◽  
Author(s):  
Jieshun Lin ◽  
Yuda Purwana Roswanjaya ◽  
Wouter Kohlen ◽  
Jens Stougaard ◽  
Dugald Reid
Keyword(s):  
Nitrogen Fixation ◽  
Developmental Process ◽  
Root Zone ◽  
Lotus Japonicus ◽  
Nodule Development ◽  
Nodule Formation ◽  
Dependent Manner ◽  
Concentration Dependent Manner ◽  
Cytokinin Biosynthesis ◽  
Nitrate Inhibition

AbstractLegumes balance nitrogen acquisition from soil nitrate with symbiotic nitrogen fixation. Nitrogen fixation requires establishment of a new organ, which is a cytokinin dependent developmental process in the root. We found cytokinin biosynthesis is a central integrator, balancing nitrate signalling with symbiotic acquired nitrogen. Low nitrate conditions provide a permissive state for induction of cytokinin by symbiotic signalling and thus nodule development. In contrast, high nitrate is inhibitory to cytokinin accumulation and nodule establishment in the root zone susceptible to nodule formation. This reduction of symbiotic cytokinin accumulation was further exacerbated in cytokinin biosynthesis mutants, which display hypersensitivity to nitrate inhibition of nodule development, maturation and nitrogen fixation. Consistent with this, cytokinin application can rescue nodulation and nitrogen fixation of biosynthesis mutants in a concentration dependent manner. These inhibitory impacts of nitrate on symbiosis occur in a Nlp1 and Nlp4 dependent manner and contrast with the positive influence of nitrate on cytokinin biosynthesis that occurs in non-symbiotic species. Altogether this shows that legumes, as exemplified by Lotus japonicus, have evolved a different cytokinin response to nitrate compared to non-legumes.One sentence summaryCytokinin biosynthesis is suppressed by nitrate in Lotus japonicus, providing a mechanism for nitrate inhibition of symbiotic nodule organogenesis.

scholarly journals Nitrate restricts nodule organogenesis through inhibition of cytokinin biosynthesis in Lotus japonicus

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Jieshun Lin ◽  
Yuda Purwana Roswanjaya ◽  
Wouter Kohlen ◽  
Jens Stougaard ◽  
Dugald Reid
Keyword(s):  
Nitrogen Fixation ◽  
Developmental Process ◽  
Root Zone ◽  
Root Nodules ◽  
Lotus Japonicus ◽  
Nodule Development ◽  
Nodule Formation ◽  
Dependent Manner ◽  
Concentration Dependent Manner ◽  
Cytokinin Biosynthesis

AbstractLegumes balance nitrogen acquisition from soil nitrate with symbiotic nitrogen fixation. Nitrogen fixation requires establishment of a new organ, which is a cytokinin dependent developmental process in the root. We found cytokinin biosynthesis is a central integrator, balancing nitrate signalling with symbiotic acquired nitrogen. Low nitrate conditions provide a permissive state for induction of cytokinin by symbiotic signalling and thus nodule development. In contrast, high nitrate is inhibitory to cytokinin accumulation and nodule establishment in the root zone susceptible to nodule formation. This reduction of symbiotic cytokinin accumulation was further exacerbated in cytokinin biosynthesis mutants, which display hypersensitivity to nitrate inhibition of nodule development, maturation and nitrogen fixation. Consistent with this, cytokinin application rescues nodulation and nitrogen fixation of biosynthesis mutants in a concentration dependent manner. These inhibitory impacts of nitrate on symbiosis occur in a Nlp1 and Nlp4 dependent manner and contrast with the positive influence of nitrate on cytokinin biosynthesis that occurs in species that do not form symbiotic root nodules. Altogether this shows that legumes, as exemplified by Lotus japonicus, have evolved a different cytokinin response to nitrate compared to non-legumes.

scholarly journals Sinorhizobium meliloti nfe (Nodulation Formation Efficiency) Genes Exhibit Temporal and Spatial Expression Patterns Similar to Those of Genes Involved in Symbiotic Nitrogen Fixation

2000 ◽  
Vol 13 (6) ◽  
pp. 583-591 ◽  
Author(s):  
Fernando M. García-Rodríguez ◽  
Nicolás Toro
Keyword(s):  
Nitrogen Fixation ◽  
Sinorhizobium Meliloti ◽  
Symbiotic Nitrogen Fixation ◽  
Expression Patterns ◽  
Nodule Development ◽  
Spatial Expression ◽  
Consensus Sequences ◽  
Promoter Sequences ◽  
Meliloti Strain ◽  
Temporal And Spatial

The nfe genes (nfeA, nfeB, and nfeD) are involved in the nodulation efficiency and competitiveness of the Sinorhizobium meliloti strain GR4 on alfalfa roots. The nfeA and nfeB genes are preceded by functional nif consensus sequences and NifA binding motifs. Here, we determined the temporal and spatial expression patterns of the nfe genes in symbiosis with alfalfa. Translational fusions of the nfe promoters with the gusA gene and reverse transcription-polymerase chain reaction analyses indicate that they are expressed and translated within mature nitrogen-fixing nodules and not during early steps of nodule development. Within the nodules the three nfe genes exhibit a spatial expression pattern similar to that of genes involved in symbiotic nitrogen fixation. We show that nfeB and nfeD genes are expressed not only from their own promoters but also from the upstream nfe promoter sequences. Furthermore, with the use of specific antibodies the NfeB and NfeD proteins were detected within the root nodule bac-teroid fraction. Finally, NfeB was inmunolocalized in the bacteroid cell membrane whereas NfeD was detected in the bacteroid cytoplasm.

scholarly journals Laser Microdissection of Pisum sativum L. Nodules Followed by RNA-Seq Analysis Revealed Crucial Transcriptomic Changes During Infected Cell Differentiation

Agronomy ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 2504
Author(s):  
Pyotr G. Kusakin ◽  
Tatiana A. Serova ◽  
Natalia E. Gogoleva ◽  
Yuri V. Gogolev ◽  
Viktor E. Tsyganov
Keyword(s):  
Nitrogen Fixation ◽  
Pisum Sativum ◽  
Laser Microdissection ◽  
Host Cells ◽  
Nodule Development ◽  
Nodule Formation ◽  
Rna Seq ◽  
Legume Crop ◽  
Pisum Sativum L ◽  
Transcriptional Changes

Garden pea (Pisum sativum L.) is a globally important legume crop. Like other legumes, it forms beneficial symbiotic interactions with the soil bacteria rhizobia, gaining the ability to fix atmospheric nitrogen. In pea nodules, the meristem is long-lasting and results in the formation of several histological zones that implicate a notable differentiation of infected host cells. However, the fine transcriptional changes that accompany differentiation are still unknown. In this study, using laser microdissection followed by RNA-seq analysis, we performed transcriptomic profiling in the early infection zone, late infection zone, and nitrogen fixation zone of 11-day-old nodules of pea wild-type line SGE. As a result, a list of functional groups of differentially expressed genes (DEGs) in different nodule histological zones and a list of genes with the most prominent expression changes during nodule development were obtained. Their analyses demonstrated that the highest amount of DEGs was associated with the nitrogen fixation zone. Among well-known genes controlling nodule development, we revealed genes that can be novel players throughout nodule formation. The characterized genes in pea were compared with those previously described in other legumes and their possible functions in nodule development are discussed.

scholarly journals Molecular Characterization of Carbonic Anhydrase Genes in Lotus japonicus and Their Potential Roles in Symbiotic Nitrogen Fixation

2021 ◽  
Vol 22 (15) ◽  
pp. 7766
Author(s):  
Longlong Wang ◽  
Jianjun Liang ◽  
Yu Zhou ◽  
Tao Tian ◽  
Baoli Zhang ◽  
...  
Keyword(s):  
Nitrogen Fixation ◽  
Carbonic Anhydrase ◽  
Root Nodule ◽  
Higher Plants ◽  
Expression Patterns ◽  
Lotus Japonicus ◽  
Nodule Development ◽  
Model Legume ◽  
N Assimilation ◽  
Mature Nodule

Carbonic anhydrase (CA) plays a vital role in photosynthetic tissues of higher plants, whereas its non-photosynthetic role in the symbiotic root nodule was rarely characterized. In this study, 13 CA genes were identified in the model legume Lotus japonicus by comparison with Arabidopsis CA genes. Using qPCR and promoter-reporter fusion methods, three previously identified nodule-enhanced CA genes (LjαCA2, LjαCA6, and LjβCA1) have been further characterized, which exhibit different spatiotemporal expression patterns during nodule development. LjαCA2 was expressed in the central infection zone of the mature nodule, including both infected and uninfected cells. LjαCA6 was restricted to the vascular bundle of the root and nodule. As for LjβCA1, it was expressed in most cell types of nodule primordia but only in peripheral cortical cells and uninfected cells of the mature nodule. Using CRISPR/Cas9 technology, the knockout of LjβCA1 or both LjαCA2 and its homolog, LjαCA1, did not result in abnormal symbiotic phenotype compared with the wild-type plants, suggesting that LjβCA1 or LjαCA1/2 are not essential for the nitrogen fixation under normal symbiotic conditions. Nevertheless, the nodule-enhanced expression patterns and the diverse distributions in different types of cells imply their potential functions during root nodule symbiosis, such as CO2 fixation, N assimilation, and pH regulation, which await further investigations.

scholarly journals Identification of the Important Genes of Bradyrhizobium diazoefficiens 113-2 Involved in Soybean Nodule Development and Senescence

2021 ◽  
Vol 12 ◽  
Author(s):  
Songli Yuan ◽  
Shunxin Zhou ◽  
Yong Feng ◽  
Chanjuan Zhang ◽  
Yi Huang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Nitrogen Fixation ◽  
Molecular Mechanisms ◽  
High Efficiency ◽  
Developmental Stages ◽  
Expression Patterns ◽  
Fertilizer Application ◽  
Nodule Development ◽  
Molecular Events ◽  
Symbiotic Functioning

Legume nodule development and senescence directly affect nitrogen fixation efficiency and involve a programmed series of molecular events. These molecular events are carried out synchronously by legumes and rhizobia. The characteristics and molecular mechanisms of nitrogen fixation at soybean important developmental stages play critical roles in soybean cultivation and fertilizer application. Although the gene expression of soybean were analyzed in nodules at five important soybean developmental stages, information on the expression of rhizobial genes in these nodule samples is limited. In the present study, we investigated the expression of Bradyrhizobium diazoefficiens 113-2 genes in the nodule samples from five developmental stages of soybean (Branching stage, flowering stage, fruiting stage, pod stage and harvest stage). Similar gene expression patterns of B. diazoefficiens 113-2 were existed during optimal symbiotic functioning, while different expression patterns were found among early nodule development, nitrogen fixation progress and nodule senescence. Besides, we identified 164 important different expression genes (DEGs) associated with nodule development and senescence. These DEGs included those encoding nod, nif, fix proteins and T3SS secretion system-related proteins, as well as proteins involved in nitrogen metabolism, ABC transporters and two-component system pathways. Gene Ontology, KEGG pathway and homology analysis of the identified DEGs revealed that most of these DEGs are uncharacterized genes associated with nodule development and senescence, and they are not core genes among the rhizobia genomes. Our results provide new clues for the understanding of the genetic determinants of soil rhizobia in nodule development and senescence, and supply theoretical basis for the creation of high efficiency soybean cultivation technology.

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