An integrated physical, genetic and cytogenetic map around the sunn locus of Medicago truncatula

Genome ◽  
2003 ◽  
Vol 46 (4) ◽  
pp. 665-672 ◽  
Author(s):  
E Schnabel ◽  
O Kulikova ◽  
R V Penmetsa ◽  
T Bisseling ◽  
D R Cook ◽  
...  
Keyword(s):  
Genetic Distance ◽  
Medicago Truncatula ◽  
Genetic Map ◽  
Sinorhizobium Meliloti ◽  
Chromosome Region ◽  
Single Gene ◽  
Artificial Chromosome ◽  
Cytogenetic Map ◽  
Bac Contig ◽  
Group 4

The sunn mutation of Medicago truncatula is a single-gene mutation that confers a novel supernodulation phenotype in response to inoculation with Sinorhizobium meliloti. We took advantage of the publicly available codominant PCR markers, the high-density genetic map, and a linked cytogenetic map to define the physical and genetic region containing sunn. We determined that sunn is located at the bottom of linkage group 4, where a fine-structure genetic map was used to place the locus within a ~400-kb contig of bacterial artificial chromosome (BAC) clones. Genetic analyses of the sunn contig, as well as of a second, closely linked BAC contig designated NUM1, indicate that the physical to genetic distance within this chromosome region is in the range of 1000 –1100 kb·cM–1. The ratio of genetic to cytogenetic distance determined across the entire region is 0.3 cM·μm–1. These estimates are in good agreement with the empirically determined value of ~300 kb·μm–1 measured for the NUM1 contig. The assignment of sunn to a defined physical interval should provide a basis for sequencing and ultimately cloning the responsible gene.Key words: FISH, physical to genetic distance, Medicago truncatula, map-based cloning.

Comparative physical mapping reveals features of microsynteny between Glycine max, Medicago truncatula, and Arabidopsis thaliana

Genome ◽  
2004 ◽  
Vol 47 (1) ◽  
pp. 141-155 ◽  
Author(s):  
H H Yan ◽  
J Mudge ◽  
D-J Kim ◽  
R C Shoemaker ◽  
D R Cook ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Glycine Max ◽  
Medicago Truncatula ◽  
Physical Mapping ◽  
Large Scale ◽  
Sequence Similarity ◽  
Artificial Chromosome ◽  
Bac Contig ◽  
Cross Hybridization ◽  
Bac Contigs

To gain insight into genomic relationships between soybean (Glycine max) and Medicago truncatula, eight groups of bacterial artificial chromosome (BAC) contigs, together spanning 2.60 million base pairs (Mb) in G. max and 1.56 Mb in M. truncatula, were compared through high-resolution physical mapping combined with sequence and hybridization analysis of low-copy BAC ends. Cross-hybridization among G. max and M. truncatula contigs uncovered microsynteny in six of the contig groups and extensive microsynteny in three. Between G. max homoeologous (within genome duplicate) contigs, 85% of coding and 75% of noncoding sequences were conserved at the level of cross-hybridization. By contrast, only 29% of sequences were conserved between G. max and M. truncatula, and some kilobase-scale rearrangements were also observed. Detailed restriction maps were constructed for 11 contigs from the three highly microsyntenic groups, and these maps suggested that sequence order was highly conserved between G. max duplicates and generally conserved between G. max and M. truncatula. One instance of homoeologous BAC contigs in M. truncatula was also observed and examined in detail. A sequence similarity search against the Arabidopsis thaliana genome sequence identified up to three microsyntenic regions in A. thaliana for each of two of the legume BAC contig groups. Together, these results confirm previous predictions of one recent genome-wide duplication in G. max and suggest that M. truncatula also experienced ancient large-scale genome duplications.Key words: Glycine max, Medicago truncatula, Arabidopsis thaliana, conserved microsynteny, genome duplication.

scholarly journals Genetic and Physical Mapping of the RPP13 Locus, in Arabidopsis, Responsible for Specific Recognition of Several Peronospora parasitica (Downy Mildew) Isolates

1999 ◽  
Vol 12 (9) ◽  
pp. 792-802 ◽  
Author(s):  
Peter Bittner-Eddy ◽  
Canan Can ◽  
Nick Gunn ◽  
Matthieu Pinel ◽  
Mahmut Tör ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Bacterial Artificial Chromosome ◽  
Downy Mildew ◽  
Physical Mapping ◽  
Single Gene ◽  
Artificial Chromosome ◽  
Chromosome 3 ◽  
Peronospora Parasitica ◽  
Bac Contig ◽  
Recognition Capability

Fifteen isolates of the biotrophic oomycete Peronospora parasitica (downy mildew) were obtained from a population of Arabidopsis thaliana plants that established naturally in a garden the previous year. They exhibited phenotypic variation in a set of 12 Arabidopsis accessions that suggested that the parasite population consisted of at least six pathotypes. One isolate, Maks9, elicited an interaction phenotype of flecking necrosis and no sporulation (FN) in the Arabidopsis accession Nd-1, and more extensive pitting necrosis with no sporulation (PN) in the accession Ws-2. RPP13 was designated as the locus for a single dominant resistance gene associated with the resistance in Nd-1 and mapped to an interval of approximately 60 kb on a bacterial artificial chromosome (BAC) contig on the lower arm of chromosome 3. This locus is approximately 6 cM telomeric to RPP1, which was previously described as the locus for the PN interaction with five Peronospora isolates, including resistance to Maks9 in Ws-2. New Peronospora isolates were obtained from four other geographically distinct populations of P. parasitica. Four isolates were characterized that elicited an FN phenotype in Nd-1 and mapped resistance to the RPP13 locus. This suggests that the RPP13 locus contains either a single gene capable of multiple isolate recognition or a group of tightly linked genes. Further analysis suggests that the RPP11 gene in the accession Rld-0 may be allelic to RPP13 but results in a different recognition capability.

scholarly journals Expression of Medicago truncatula Genes Responsive to Nitric Oxide in Pathogenic and Symbiotic Conditions

2008 ◽  
Vol 21 (6) ◽  
pp. 781-790 ◽  
Author(s):  
Alberto Ferrarini ◽  
Matteo De Stefano ◽  
Emmanuel Baudouin ◽  
Chiara Pucciariello ◽  
Annalisa Polverari ◽  
...  
Keyword(s):  
Nitric Oxide ◽  
Medicago Truncatula ◽  
Regulatory Networks ◽  
Sinorhizobium Meliloti ◽  
Biotic Interactions ◽  
Hypersensitive Reaction ◽  
Nodule Formation ◽  
Polymorphism Analysis ◽  
Symbiotic Interaction ◽  
Physiological Relevance

Nitric oxide (NO) is involved in diverse physiological processes in plants, including growth, development, response to pathogens, and interactions with beneficial microorganisms. In this work, a dedicated microarray representing the widest database available of NO-related transcripts in plants has been produced with 999 genes identified by a cDNA amplified fragment length polymorphism analysis as modulated in Medicago truncatula roots treated with two NO donors. The microarray then was used to monitor the expression of NO-responsive genes in M. truncatula during the incompatible interaction with the foliar pathogen Colletotrichum trifolii race 1 and during the symbiotic interaction with Sinorhizobium meliloti 1021. A wide modulation of NO-related genes has been detected during the hypersensitive reaction or during nodule formation and is discussed with special emphasis on the physiological relevance of these genes in the context of the two biotic interactions. This work clearly shows that NO-responsive genes behave differently depending on the plant organ and on the type of interaction, strengthening the need to consider regulatory networks, including different signaling molecules.

scholarly journals Structure and antimicrobial activity of NCR169, a nodule-specific cysteine-rich peptide of Medicago truncatula

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Noriyoshi Isozumi ◽  
Yuya Masubuchi ◽  
Tomohiro Imamura ◽  
Masashi Mori ◽  
Hironori Koga ◽  
...  
Keyword(s):  
Antimicrobial Activity ◽  
Medicago Truncatula ◽  
Mechanism Of Action ◽  
Disulfide Bonds ◽  
Sinorhizobium Meliloti ◽  
Bound State ◽  
Disulfide Linkage ◽  
Model Legume ◽  
Nmr Structures ◽  
And Function

AbstractA model legume, Medicago truncatula, has over 600 nodule-specific cysteine-rich (NCR) peptides required for symbiosis with rhizobia. Among them, NCR169, an essential factor for establishing symbiosis, has four cysteine residues that are indispensable for its function. However, knowledge of NCR169 structure and mechanism of action is still lacking. In this study, we solved two NMR structures of NCR169 caused by different disulfide linkage patterns. We show that both structures have a consensus C-terminal β-sheet attached to an extended N-terminal region with dissimilar features; one moves widely, whereas the other is relatively stapled. We further revealed that the disulfide bonds of NCR169 contribute to its structural stability and solubility. Regarding the function, one of the NCR169 oxidized forms could bind to negatively charged bacterial phospholipids. Furthermore, the positively charged lysine-rich region of NCR169 may be responsible for its antimicrobial activity against Escherichia coli and Sinorhizobium meliloti. This active region was disordered even in the phospholipid bound state, suggesting that the disordered conformation of this region is key to its function. Morphological observations suggested the mechanism of action of NCR169 on bacteria. The present study on NCR169 provides new insights into the structure and function of NCR peptides.

scholarly journals On Genetic Map Functions

Genetics ◽  
1996 ◽  
Vol 142 (4) ◽  
pp. 1369-1377
Author(s):  
Hongyu Zhao ◽  
Terence P Speed
Keyword(s):  
Genetic Distance ◽  
Genetic Map ◽  
Probability Model ◽  
Recombination Fraction ◽  
Renewal Processes ◽  
Gamma Distributions ◽  
Multilocus Analysis ◽  
Map Function ◽  
Better Than

Abstract Various genetic map functions have been proposed to infer the unobservable genetic distance between two loci from the observable recombination fraction between them. Some map functions were found to fit data better than others. When there are more than three markers, multilocus recombination probabilities cannot be uniquely determined by the defining property of map functions, and different methods have been proposed to permit the use of map functions to analyze multilocus data. If for a given map function, there is a probability model for recombination that can give rise to it, then joint recombination probabilities can be deduced from this model. This provides another way to use map functions in multilocus analysis. In this paper we show that stationary renewal processes give rise to most of the map functions in the literature. Furthermore, we show that the interevent distributions of these renewal processes can all be approximated quite well by gamma distributions.

A physical map with yeast artificial chromosome (YAC) clones covering 63% of the 12 rice chromosomes

Genome ◽  
2001 ◽  
Vol 44 (1) ◽  
pp. 32-37 ◽  
Author(s):  
Shoko Saji ◽  
Yosuke Umehara ◽  
Baltazar A Antonio ◽  
Hiroko Yamane ◽  
Hiroshi Tanoue ◽  
...  
Keyword(s):  
Genetic Map ◽  
Dna Markers ◽  
Yeast Artificial Chromosome ◽  
Physical Map ◽  
Genome Structure ◽  
Rice Genome ◽  
Artificial Chromosome ◽  
Physical Length ◽  
Rice Chromosomes ◽  
Yac Contig

A new YAC (yeast artificial chromosome) physical map of the 12 rice chromosomes was constructed utilizing the latest molecular linkage map. The 1439 DNA markers on the rice genetic map selected a total of 1892 YACs from a YAC library. A total of 675 distinct YACs were assigned to specific chromosomal locations. In all chromosomes, 297 YAC contigs and 142 YAC islands were formed. The total physical length of these contigs and islands was estimated to 270 Mb which corresponds to approximately 63% of the entire rice genome (430 Mb). Because the physical length of each YAC contig has been measured, we could then estimate the physical distance between genetic markers more precisely than previously. In the course of constructing the new physical map, the DNA markers mapped at 0.0-cM intervals were ordered accurately and the presence of potentially duplicated regions among the chromosomes was detected. The physical map combined with the genetic map will form the basis for elucidation of the rice genome structure, map-based cloning of agronomically important genes, and genome sequencing.Key words: physical mapping, YAC contig, rice genome, rice chromosomes.

scholarly journals Inoculation with Efficient Nitrogen Fixing and Indoleacetic Acid Producing Bacterial Microsymbiont Enhance Tolerance of the Model LegumeMedicago truncatulato Iron Deficiency

2018 ◽  
Vol 2018 ◽  
pp. 1-14 ◽  
Author(s):  
Nadia Kallala ◽  
Wissal M’sehli ◽  
Karima Jelali ◽  
Zribi Kais ◽  
Haythem Mhadhbi
Keyword(s):  
Oxidative Stress ◽  
Iron Deficiency ◽  
Medicago Truncatula ◽  
Sinorhizobium Meliloti ◽  
Plant Biomass ◽  
High Growth ◽  
Fe Deficiency ◽  
Nitrogen Fixing ◽  
Bacterial Strains ◽  
Negative Effect

The aim of this study was to assess the effect of symbiotic bacteria inoculation on the response ofMedicago truncatulagenotypes to iron deficiency. The present work was conducted on threeMedicago truncatulagenotypes: A17, TN8.20, and TN1.11. Three treatments were performed: control (C), direct Fe deficiency (DD), and induced Fe deficiency by bicarbonate (ID). Plants were nitrogen-fertilized (T) or inoculated with two bacterial strains:Sinorhizobium melilotiTII7 andSinorhizobium medicaeSII4. Biometric, physiological, and biochemical parameters were analyzed. Iron deficiency had a significant lowering effect on plant biomass and chlorophyll content in allMedicago truncatulagenotypes. TN1.11 showed the highest lipid peroxidation and leakage of electrolyte under iron deficiency conditions, which suggest that TN1.11 was more affected than A17 and TN8.20 by Fe starvation. Iron deficiency affected symbiotic performance indices of allMedicago truncatulagenotypes inoculated with bothSinorhizobiumstrains, mainly nodules number and biomass as well as nitrogen-fixing capacity. Nevertheless, inoculation withSinorhizobiumstrains mitigates the negative effect of Fe deficiency on plant growth and oxidative stress compared to nitrogen-fertilized plants. The highest auxin producing strain, TII7, preserves relatively high growth and root biomass and length when inoculated to TN8.20 and A17. On the other hand, both TII7 and SII4 strains improve the performance of sensitive genotype TN1.11 through reduction of the negative effect of iron deficiency on chlorophyll and plant Fe content. The bacterial inoculation improved Fe-deficient plant response to oxidative stress via the induction of the activities of antioxidant enzymes.

scholarly journals Quorum quenching activity of the PGPR Bacillus subtilis UD1022 alters nodulation efficiency of Sinorhizobium meliloti on Medicago truncatula

2020 ◽  
Author(s):  
Amanda Rosier ◽  
Pascale B. Beauregard ◽  
Harsh P. Bais
Keyword(s):  
Bacillus Subtilis ◽  
Plant Growth ◽  
Medicago Truncatula ◽  
Sinorhizobium Meliloti ◽  
Quorum Quenching ◽  
Agricultural System ◽  
Synergistic Activity ◽  
Sustainable Solutions ◽  
Plant Growth Promoting ◽  
Growth Promoting

AbstractPlant growth promoting rhizobacteria (PGPR) have enormous potential for solving some of the myriad challenges facing our global agricultural system. Intense research efforts are rapidly moving the field forward and illuminating the wide diversity of bacteria and their plant beneficial activities. In the development of better crop solutions using these PGPR, producers are including multiple different species of PGPR in their formulations in a ‘consortia’ approach. While the intention is to emulate more natural rhizomicrobiome systems, the aspect of bacterial interactions has not been properly regarded. By using a tri-trophic model of Medicago truncatula A17 Jemalong, its nitrogen (N)-fixing symbiont Sinorhizobium meliloti Rm8530 and the PGPR Bacillus subtilis UD1022, we demonstrate indirect influences between the bacteria affecting their plant growth promoting activities. Co-cultures of UD1022 with Rm8530 significantly reduced Rm8530 biofilm formation and downregulated quorum sensing (QS) genes responsible for symbiotically active biofilm production. This work also identifies the presence and activity of a quorum quenching lactonase in UD1022 and proposes this as the mechanism for non-synergistic activity of this model ‘consortium’. These interspecies interactions may be common in the rhizosphere and are critical to understand as we seek to develop new sustainable solutions in agriculture.

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