Resistance to Subterranean clover mottle virus in Medicago truncatula and genetic mapping of a resistance locus

Subterranean clover mottle virus (SCMoV), which causes an important disease of annual clover pastures, was inoculated to the annual pasture legume Medicago truncatula, a model legume species used to help understand legume genome structure and function. Two hundred and nine accessions representing the core collection of M. truncatula were inoculated with infective sap containing SCMoV to determine their disease phenotypes. Forty-two of these accessions remained uninfected systemically and so were potentially resistant to the virus. Accession DZA315.16 developed a localised hypersensitive resistance reaction. In an F8 mapping population from a cross between the susceptible parent Jemalong 6/A17 and resistant accession DZA315.16, a total of 166 F8 recombinant inbred lines (RILs) were phenotyped for resistance and susceptibility to SCMoV. Resistant and susceptible lines showed parental phenotypic responses: 84 were susceptible and 82 were resistant, suggesting presence of a single resistance (R) gene. The phenotypic data were combined with genotypic data (76 polymorphic molecular markers) for this RIL population to provide a framework map. Genetic analysis located a single resistance locus termed RSCMoV1 on the long arm of chromosome 6. These results provide a basis for fine mapping the RSCMoV1 gene.

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

Scientific Reports ◽

10.1038/s41598-021-89485-w ◽

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.

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Comparison of genome structure between white clover and Medicago truncatula supports homoeologous group nomenclature based on conserved synteny

Genome ◽

10.1139/g08-076 ◽

2008 ◽

Vol 51 (11) ◽

pp. 905-911 ◽

Cited By ~ 14

Author(s):

Julie George ◽

Timothy I. Sawbridge ◽

Noel O.I. Cogan ◽

Anthony R. Gendall ◽

Kevin F. Smith ◽

...

Keyword(s):

Medicago Truncatula ◽

White Clover ◽

Agronomic Traits ◽

Genome Structure ◽

Draft Genome ◽

Gene Location ◽

Pasture Production ◽

Model Legume ◽

Nomenclature System ◽

Translocation Event

Computational analysis has been used to align the genetic map of white clover ( Trifolium repens L.) with the draft genome sequence of the model legume species Medicago truncatula Gaertn. In silico comparison based on white clover expressed sequence tags that contain simple sequence repeat loci revealed substantial macrosynteny between the genomes of these two species, which are closely related within the Trifolieae tribe of the Fabaceae family. Six of the eight homoeologous chromosome groups (HGs) of allotetraploid white clover show predominant relationships with single M. truncatula (Mt) chromosomes, while the two remaining groups may have participated in an evolutionary reciprocal translocation event. On this basis, a new chromosome nomenclature system for allotetraploid white clover is proposed such that HG A = 3, HG B = 8, HG C = 7, HG D = 4, HG E = 1, HG F = 2, HG G = 5, and HG H = 6. A rationalized linkage map ordering system has also been demonstrated. Improved knowledge of the relationships between agricultural and model forage legume genomes will facilitate prediction of gene location for key agronomic traits for pasture production.

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Integrated approaches to studying Medicago truncatula genome structure and function and their applications in biotechnology

Molecular Breeding ◽

10.1007/s11032-012-9729-4 ◽

2012 ◽

Vol 30 (3) ◽

pp. 1431-1442 ◽

Cited By ~ 1

Author(s):

A. S. Pires ◽

N. Geraldo ◽

T. Cerqueira ◽

R. Abranches

Keyword(s):

Medicago Truncatula ◽

Genome Structure ◽

Structure And Function ◽

Approaches To Studying ◽

Integrated Approaches ◽

And Function

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Characterization of the Interaction Between the Bacterial Wilt Pathogen Ralstonia solanacearum and the Model Legume Plant Medicago truncatula

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-20-2-0159 ◽

2007 ◽

Vol 20 (2) ◽

pp. 159-167 ◽

Cited By ~ 76

Author(s):

Fabienne Vailleau ◽

Elodie Sartorel ◽

Marie-Françoise Jardinaud ◽

Fabien Chardon ◽

Stéphane Genin ◽

...

Keyword(s):

Plant Species ◽

Medicago Truncatula ◽

Bacterial Wilt ◽

Ralstonia Solanacearum ◽

Recombinant Inbred Lines ◽

Model Legume ◽

Legume Plant ◽

Hrp Genes

The soilborne pathogen Ralstonia solanacearum is the causal agent of bacterial wilt and attacks more than 200 plant species, including some legumes and the model legume plant Medicago truncatula. We have demonstrated that M. truncatula accessions Jemalong A17 and F83005.5 are susceptible to R. solanacearum and, by screening 28 R. solana-cearum strains on the two M. truncatula lines, differential interactions were identified. R. solanacearum GMI1000 infected Jemalong A17 line, and disease symptoms were dependent upon functional hrp genes. An in vitro root inoculation method was employed to demonstrate that R. solanacearum colonized M. truncatula via the xylem and intercellular spaces. R. solanacearum multiplication was restricted by a factor greater than 1 × 105 in the resistant line F83005.5 compared with susceptible Jemalong A17. Genetic analysis of recombinant inbred lines from a cross between Jemalong A17 and F83005.5 revealed the presence of major quantitative trait loci for bacterial wilt resistance located on chromosome 5. The results indicate that the root pathosystem for M. truncatula will provide useful traits for molecular analyses of disease and resistance in this model plant species.

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Partial Resistance of Medicago truncatula to Aphanomyces euteiches Is Associated with Protection of the Root Stele and Is Controlled by a Major QTL Rich in Proteasome-Related Genes

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-22-9-1043 ◽

2009 ◽

Vol 22 (9) ◽

pp. 1043-1055 ◽

Cited By ~ 55

Author(s):

Naceur Djébali ◽

Alain Jauneau ◽

Carine Ameline-Torregrosa ◽

Fabien Chardon ◽

Valérie Jaulneau ◽

...

Keyword(s):

Medicago Truncatula ◽

Partial Resistance ◽

Recombinant Inbred Lines ◽

Isogenic Line ◽

Aphanomyces Euteiches ◽

Model Legume ◽

Trait Locus ◽

Rot Disease ◽

Root Stele

A pathosystem between Aphanomyces euteiches, the causal agent of pea root rot disease, and the model legume Medicago truncatula was developed to gain insights into mechanisms involved in resistance to this oomycete. The F83005.5 French accession and the A17-Jemalong reference line, susceptible and partially resistant, respectively, to A. euteiches, were selected for further cytological and genetic analyses. Microscopy analyses of thin root sections revealed that a major difference between the two inoculated lines occurred in the root stele, which remained pathogen free in A17. Striking features were observed in A17 roots only, including i) frequent pericycle cell divisions, ii) lignin deposition around the pericycle, and iii) accumulation of soluble phenolic compounds. Genetic analysis of resistance was performed on an F7 population of 139 recombinant inbred lines and identified a major quantitative trait locus (QTL) near the top of chromosome 3. A second study, with near-isogenic line responses to A. euteiches confirmed the role of this QTL in expression of resistance. Fine-mapping allowed the identification of a 135-kb sequenced genomic DNA region rich in proteasome-related genes. Most of these genes were shown to be induced only in inoculated A17. Novel mechanisms possibly involved in the observed partial resistance are proposed.

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AER1, a Major Gene Conferring Resistance to Aphanomyces euteiches in Medicago truncatula

Phytopathology ◽

10.1094/phyto-99-2-0203 ◽

2009 ◽

Vol 99 (2) ◽

pp. 203-208 ◽

Cited By ~ 26

Author(s):

M.-L. Pilet-Nayel ◽

J.-M. Prospéri ◽

C. Hamon ◽

A. Lesné ◽

R. Lecointe ◽

...

Keyword(s):

Resistance Gene ◽

Medicago Truncatula ◽

Recombinant Inbred Lines ◽

Major Gene ◽

Genetic System ◽

Broad Host Range ◽

Aphanomyces Euteiches ◽

Model Legume ◽

Leguminous Crops ◽

Gene Rich Region

Aphanomyces euteiches is a major soilborne oomycete pathogen that infects various legume species, including pea and alfalfa. The model legume Medicago truncatula has recently emerged as a valuable genetic system for understanding the genetic basis of resistance to A. euteiches in leguminous crops. The objective of this study was to identify genetic determinants of resistance to a broad host-range pea-infecting strain of A. euteiches in M. truncatula. Two M. truncatula segregating populations of 178 F5 recombinant inbred lines and 200 F3 families from the cross F83005.5 (susceptible) × DZA045.5 (resistant) were screened for resistance to A. euteiches. Phenotypic distributions observed suggested a dominant monogenic control of resistance. A major locus associated with resistance to A. euteiches, namely AER1, was mapped by bulk segregant analysis to a terminal end of chromosome 3 in M. truncatula and explained 88% of the phenotypic variation. AER1 was identified in a resistance-gene-rich region, where resistance gene analogs and genes associated with disease resistance phenotypes have been identified. Discovery of AER1 opens up new prospects for improving resistance to A. euteiches in cultivated legumes using a comparative genomics approach.

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Impact of DNA methylation on 3D genome structure

Nature Communications ◽

10.1038/s41467-021-23142-8 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Diana Buitrago ◽

Mireia Labrador ◽

Juan Pablo Arcon ◽

Rafael Lema ◽

Oscar Flores ◽

...

Keyword(s):

Dna Methylation ◽

Chromatin Structure ◽

Chromatin Condensation ◽

Genome Structure ◽

Dna Methyltransferases ◽

Model System ◽

Structure And Function ◽

3D Genome ◽

Cellular Machinery ◽

And Function

AbstractDetermining the effect of DNA methylation on chromatin structure and function in higher organisms is challenging due to the extreme complexity of epigenetic regulation. We studied a simpler model system, budding yeast, that lacks DNA methylation machinery making it a perfect model system to study the intrinsic role of DNA methylation in chromatin structure and function. We expressed the murine DNA methyltransferases in Saccharomyces cerevisiae and analyzed the correlation between DNA methylation, nucleosome positioning, gene expression and 3D genome organization. Despite lacking the machinery for positioning and reading methylation marks, induced DNA methylation follows a conserved pattern with low methylation levels at the 5’ end of the gene increasing gradually toward the 3’ end, with concentration of methylated DNA in linkers and nucleosome free regions, and with actively expressed genes showing low and high levels of methylation at transcription start and terminating sites respectively, mimicking the patterns seen in mammals. We also see that DNA methylation increases chromatin condensation in peri-centromeric regions, decreases overall DNA flexibility, and favors the heterochromatin state. Taken together, these results demonstrate that methylation intrinsically modulates chromatin structure and function even in the absence of cellular machinery evolved to recognize and process the methylation signal.

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On the origin and evolutionary consequences of gene body DNA methylation

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1604666113 ◽

2016 ◽

Vol 113 (32) ◽

pp. 9111-9116 ◽

Cited By ~ 149

Author(s):

Adam J. Bewick ◽

Lexiang Ji ◽

Chad E. Niederhuth ◽

Eva-Maria Willing ◽

Brigitte T. Hofmeister ◽

...

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Recombinant Inbred Lines ◽

Dna Methyltransferases ◽

Inbred Lines ◽

Gene Body ◽

Gene Body Methylation ◽

Eutrema Salsugineum ◽

And Function ◽

Evolutionary Consequences

In plants, CG DNA methylation is prevalent in the transcribed regions of many constitutively expressed genes (gene body methylation; gbM), but the origin and function of gbM remain unknown. Here we report the discovery that Eutrema salsugineum has lost gbM from its genome, to our knowledge the first instance for an angiosperm. Of all known DNA methyltransferases, only CHROMOMETHYLASE 3 (CMT3) is missing from E. salsugineum. Identification of an additional angiosperm, Conringia planisiliqua, which independently lost CMT3 and gbM, supports that CMT3 is required for the establishment of gbM. Detailed analyses of gene expression, the histone variant H2A.Z, and various histone modifications in E. salsugineum and in Arabidopsis thaliana epigenetic recombinant inbred lines found no evidence in support of any role for gbM in regulating transcription or affecting the composition and modification of chromatin over evolutionary timescales.

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Wheat genome structure and function: genome sequence data and the International Wheat Genome Sequencing Consortium

Australian Journal of Agricultural Research ◽

10.1071/ar06155 ◽

2007 ◽

Vol 58 (6) ◽

pp. 470 ◽

Cited By ~ 11

Author(s):

P. Moolhuijzen ◽

D. S. Dunn ◽

M. Bellgard ◽

M. Carter ◽

J. Jia ◽

...

Keyword(s):

Genome Sequencing ◽

Physical Map ◽

Genome Structure ◽

Genetic Research ◽

Structure And Function ◽

Wheat Genome ◽

D Genome ◽

Genome Sequencing Consortium ◽

And Function ◽

Bac Contigs

Genome sequencing and the associated bioinformatics is now a widely accepted research tool for accelerating genetic research and the analysis of genome structure and function of wheat because it leverages similar work from other crops and plants. The International Wheat Genome Sequencing Consortium addresses the challenge of wheat genome structure and function and builds on the research efforts of Professor Bob McIntosh in the genetics of wheat. Currently, expressed sequence tags (ESTs; ~500 000 to date) are the largest sequence resource for wheat genome analyses. It is estimated that the gene coverage of the wheat EST collection is ~60%, close to that of Arabidopsis, indicating that ~40% of wheat genes are not represented in EST collections. The physical map of the D-genome donor species Aegilops tauschii is under construction (http://wheat.pw.usda.gov/PhysicalMapping). The technologies developed in this analysis of the D genome provide a good model for the approach to the entire wheat genome, namely compiling BAC contigs, assigning these BAC contigs to addresses in a high resolution genetic map, filling in gaps to obtain the entire physical length of a chromosome, and then large-scale sequencing.

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