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1.
Plant Mol Biol ; 82(4-5): 367-74, 2013 Jul.
Article in English | MEDLINE | ID: mdl-23657790

ABSTRACT

RCT1 is a TIR-NBS-LRR-type resistance (R) gene in Medicago truncatula that confers resistance to multiple races of Colletotrichum trifolii, a hemi-biotrophic fungal pathogen that causes anthracnose disease in Medicago and other closely related legumes. RCT1 undergoes alternative splicing at both coding and 3'-untranslated regions, thereby producing multiple transcript variants in its expression profile. Alternative splicing of RCT1 in the coding region results from the retention of intron 4. Because intron 4 lies downstream of the LRR-encoding exons and contains an in-frame stop codon, the alternative transcript is predicted to encode a truncated protein consisting of the entire portion of the TIR, NBS, and LRR domains but lacks the C-terminal domain of the full-length RCT1 protein encoded by the regular transcript. Here we provide evidence that the RCT1-mediated disease resistance requires the combined presence of the regular and alternative transcripts. Neither the regular nor the alternative RCT1 transcript alone is sufficient to confer resistance against the pathogen. This study, in addition to the reports on the tobacco N and Arabidopsis RPS4 genes, adds another significant example showing the involvement of alternative splicing in R gene-mediated plant immunity.


Subject(s)
Alternative Splicing/physiology , Disease Resistance/physiology , Medicago truncatula/genetics , Medicago truncatula/microbiology , Plant Proteins/genetics , Alternative Splicing/genetics , Colletotrichum/pathogenicity , Disease Resistance/genetics , Plant Diseases/genetics , Plant Diseases/microbiology , Plant Proteins/metabolism
2.
Front Plant Sci ; 3: 185, 2012.
Article in English | MEDLINE | ID: mdl-22936937

ABSTRACT

Nicotiana langsdorffii is one of two species of Nicotiana known to express an incompatible interaction with the oomycete Peronospora tabacina, the causal agent of tobacco blue mold disease. We previously showed that incompatibility is due to the hypersensitive response (HR), and plants expressing the HR are resistant to P. tabacina at all stages of growth. Resistance is due to a single dominant gene in N. langsdorffii accession S-4-4 that we have named NlRPT. In further characterizing this unique host-pathogen interaction, NlRPT has been placed on a preliminary genetic map of the N. langsdorffii genome. Allelic scores for five classes of DNA markers were determined for 90 progeny of a "modified backcross" involving two N. langsdorffii inbred lines and the related species N. forgetiana. All markers had an expected segregation ratio of 1:1, and were scored in a common format. The map was constructed with JoinMap 3.0, and loci showing excessive transmission distortion were removed. The linkage map consists of 266 molecular marker loci defined by 217 amplified fragment length polymorphisms (AFLPs), 26 simple-sequence repeats (SSRs), 10 conserved orthologous sequence markers, nine inter-simple sequence repeat markers, and four target region amplification polymorphism markers arranged in 12 linkage groups with a combined length of 1062 cM. NlRPT is located on linkage group three, flanked by four AFLP markers and one SSR. Regions of skewed segregation were detected on LGs 1, 5, and 9. Markers developed for N. langsdorffii are potentially useful genetic tools for other species in Nicotiana section Alatae, as well as in N. benthamiana. We also investigated whether AFLPs could be used to infer genetic relationships within N. langsdorffii and related species from section Alatae. A phenetic analysis of the AFLP data showed that there are two main lineages within N. langsdorffii, and that both contain populations expressing dominant resistance to P. tabacina.

3.
Proc Natl Acad Sci U S A ; 107(43): 18735-40, 2010 Oct 26.
Article in English | MEDLINE | ID: mdl-20937853

ABSTRACT

Leguminous plants can enter into root nodule symbioses with nitrogen-fixing soil bacteria known as rhizobia. An intriguing but still poorly understood property of the symbiosis is its host specificity, which is controlled at multiple levels involving both rhizobial and host genes. It is widely believed that the host specificity is determined by specific recognition of bacterially derived Nod factors by the cognate host receptor(s). Here we describe the positional cloning of two soybean genes Rj2 and Rfg1 that restrict nodulation with specific strains of Bradyrhizobium japonicum and Sinorhizobium fredii, respectively. We show that Rj2 and Rfg1 are allelic genes encoding a member of the Toll-interleukin receptor/nucleotide-binding site/leucine-rich repeat (TIR-NBS-LRR) class of plant resistance (R) proteins. The involvement of host R genes in the control of genotype-specific infection and nodulation reveals a common recognition mechanism underlying symbiotic and pathogenic host-bacteria interactions and suggests the existence of their cognate avirulence genes derived from rhizobia. This study suggests that establishment of a root nodule symbiosis requires the evasion of plant immune responses triggered by rhizobial effectors.


Subject(s)
Fabaceae/genetics , Fabaceae/microbiology , Genes, Plant , Rhizobium/genetics , Symbiosis/genetics , Base Sequence , Bradyrhizobium/genetics , Cloning, Molecular , DNA, Plant/genetics , Evolution, Molecular , Fabaceae/metabolism , Genes, Bacterial , Genetic Complementation Test , Molecular Sequence Data , Mutation , Nitrogen Fixation , Plant Proteins/genetics , RNA Interference , Sinorhizobium fredii/genetics , Glycine max/genetics , Glycine max/microbiology
4.
Plant Physiol ; 149(1): 306-17, 2009 Jan.
Article in English | MEDLINE | ID: mdl-18978069

ABSTRACT

Root symbioses with arbuscular mycorrhizal fungi and rhizobial bacteria share a common signaling pathway in legumes. Among the common symbiosis genes are CASTOR and POLLUX, the twin homologous genes in Lotus japonicus that encode putative ion channel proteins. Here, we show that the orthologs of CASTOR and POLLUX are ubiquitously present and highly conserved in both legumes and nonlegumes. Using rice (Oryza sativa) as a study system, we employ reverse genetic tools (knockout mutants and RNA interference) to demonstrate that Os-CASTOR and Os-POLLUX are indispensable for mycorrhizal symbiosis in rice. Furthermore, a cross-species complementation test indicates that Os-POLLUX can restore nodulation, but not rhizobial infection, to a Medicago truncatula dmi1 mutant.


Subject(s)
Evolution, Molecular , Oryza/genetics , Plant Proteins/metabolism , Symbiosis/genetics , Amino Acid Sequence , DNA, Bacterial/genetics , Gene Expression Regulation, Plant , Gene Knockout Techniques , Genes, Plant , Genetic Complementation Test , Medicago truncatula/genetics , Medicago truncatula/metabolism , Medicago truncatula/microbiology , Molecular Sequence Data , Mutagenesis, Insertional , Mycorrhizae/physiology , Oryza/metabolism , Oryza/microbiology , Phylogeny , Plant Proteins/genetics , Plants, Genetically Modified/genetics , Plants, Genetically Modified/metabolism , Plants, Genetically Modified/microbiology , RNA Interference , RNA, Plant/genetics , Root Nodules, Plant/microbiology , Sequence Alignment
5.
Plant Cell Rep ; 28(4): 649-61, 2009 Apr.
Article in English | MEDLINE | ID: mdl-19112567

ABSTRACT

We sequenced five BAC clones of Brassica oleracea doubled haploid 'Early Big' broccoli containing major genes in the aliphatic glucosinolate pathway, and comparatively analyzed them with similar sequences in A. thaliana and B. rapa. Additionally, we included in the analysis published sequences from three other B. oleracea BAC clones and a contig of this species corresponding to segments in A. thaliana chromosomes IV and V. A total of 2,946 kb of B. oleracea, 1,069 kb of B. rapa sequence and 2,607 kb of A. thaliana sequence were compared and analyzed. We found conserved collinearity for gene order and content restricted to specific chromosomal segments, but breaks in collinearity were frequent resulting in gene absence likely not due to gene loss but rearrangements. B. oleracea has the lowest gene density of the three species, followed by B. rapa. The genome expansion of the Brassica species, B. oleracea in particular, is due to larger introns and gene spacers resulting from frequent insertion of DNA transposons and retrotransposons. These findings are discussed in relation to the possible origin and evolution of the Brassica genomes.


Subject(s)
Arabidopsis/genetics , Brassica/genetics , Comparative Genomic Hybridization , Sequence Analysis, DNA/methods , Chromosome Mapping , Chromosomes, Artificial, Bacterial , Chromosomes, Plant/genetics , Conserved Sequence , DNA Transposable Elements , DNA, Plant/genetics , Evolution, Molecular , Genome, Plant , Glucosinolates/genetics
6.
Proc Natl Acad Sci U S A ; 105(34): 12164-9, 2008 Aug 26.
Article in English | MEDLINE | ID: mdl-18719113

ABSTRACT

Alfalfa is economically the most important forage legume worldwide. A recurrent challenge to alfalfa production is the significant yield loss caused by disease. Although knowledge of molecular mechanisms underlying host resistance should facilitate the genetic improvement of alfalfa, the acquisition of such knowledge is hampered by alfalfa's tetrasomic inheritance and outcrossing nature. However, alfalfa is congeneric with the reference legume Medicago truncatula, providing an opportunity to use M. truncatula as a surrogate to clone the counterparts of many agronomically important genes in alfalfa. In particular, the high degree of sequence identity and remarkably conserved genome structure and function between the two species enables M. truncatula genes to be used directly in alfalfa improvement. Here we report the map-based cloning of RCT1, a host resistance (R) gene in M. truncatula that confers resistance to multiple races of Colletotrichum trifolii, a hemibiotrophic fungal pathogen that causes anthracnose disease of alfalfa. RCT1 is a member of the Toll-interleukin-1 receptor/nucleotide-binding site/leucine-rich repeat (TIR-NBS-LRR) class of plant R genes and confers broad-spectrum anthracnose resistance when transferred into susceptible alfalfa plants. Thus, RCT1 provides a novel resource to develop anthracnose-resistant alfalfa cultivars and contributes to our understanding of host resistance against the fungal genus Colletotrichum. This work demonstrates the potential of using M. truncatula genes for genetic improvement of alfalfa.


Subject(s)
Genes, Plant/immunology , Medicago sativa/genetics , Medicago truncatula/genetics , Plant Diseases/immunology , Receptors, Interleukin-1/genetics , Cloning, Molecular , Colletotrichum/immunology , Medicago truncatula/immunology , Molecular Sequence Data , Plant Diseases/microbiology , Plants, Genetically Modified
7.
Plant Physiol ; 145(4): 1619-28, 2007 Dec.
Article in English | MEDLINE | ID: mdl-17965173

ABSTRACT

In natural ecosystems, many plants are able to establish mutually beneficial symbioses with microorganisms. Of critical importance to sustainable agriculture are the symbioses formed between more than 80% of terrestrial plants and arbuscular mycorrhizal (AM) fungi and between legumes and nitrogen-fixing rhizobial bacteria. Interestingly, the two symbioses share overlapping signaling pathways in legumes, suggesting that the evolutionarily recent root nodule symbiosis may have acquired functions from the ancient AM symbiosis. The Medicago truncatula DMI3 (DOESN'T MAKE INFECTIONS3) gene (MtDMI3) and its orthologs in legumes are required for both bacterial and fungal symbioses. MtDMI3 encodes a Ca(2+)/calmodulin-dependent protein kinase (CCaMK) essential for the transduction of the Ca(2+) signal induced by the perception of Nod factors. Putative orthologs of MtDMI3 are also present in non-legumes, but their function in AM symbiosis has not been demonstrated in any non-legume species. Here, we combine reverse genetic approaches and a cross-species complementation test to characterize the function of the rice (Oryza sativa) ortholog of MtDMI3, namely, OsDMI3, in AM symbiosis. We demonstrate that OsDMI3 is not only required for AM symbiosis in rice but also is able to complement a M. truncatula dmi3 mutant, indicating an equivalent role of MtDMI3 orthologs in non-legumes.


Subject(s)
Calcium-Calmodulin-Dependent Protein Kinases/genetics , Medicago truncatula/genetics , Mycorrhizae/physiology , Oryza/microbiology , Symbiosis/genetics , Amino Acid Sequence , Genetic Complementation Test , Molecular Sequence Data , Mutagenesis, Insertional , Oryza/enzymology , Oryza/genetics , Phenotype , Sequence Homology
8.
Theor Appl Genet ; 116(1): 45-52, 2007 Dec.
Article in English | MEDLINE | ID: mdl-17891371

ABSTRACT

Anthracnose of alfalfa, caused by the fungal pathogen Colletotrichum trifolii, is one of the most destructive diseases of alfalfa worldwide. An improved understanding of the genetic and molecular mechanisms underlying host resistance will facilitate the development of resistant alfalfa cultivars, thus providing the most efficient and environmentally sound strategy to control alfalfa diseases. Unfortunately, cultivated alfalfa has an intractable genetic system because of its tetrasomic inheritance and out-crossing nature. Nevertheless, the model legume Medicago truncatula, a close relative of alfalfa, has the potential to serve as a surrogate to map and clone the counterparts of agronomically important genes in alfalfa -- particularly, disease resistance genes against economically important pathogens. Here we describe the high-resolution genetic and physical mapping of RCT1, a host resistance gene against C. trifolii race 1 in M. truncatula. We have delimited the RCT1 locus within a physical interval spanning approximately 200 kb located on the top of M. truncatula linkage group 4. RCT1 is part of a complex locus containing numerous genes homologous to previously characterized TIR-NBS-LRR type resistance genes. The result presented in this paper will facilitate the positional cloning of RCT1 in Medicago.


Subject(s)
Colletotrichum/pathogenicity , Genes, Plant/genetics , Immunity, Innate/genetics , Medicago truncatula/genetics , Medicago truncatula/microbiology , Plant Diseases/genetics , Chromosome Mapping , Chromosome Segregation , Genetic Markers , Microsatellite Repeats
9.
Theor Appl Genet ; 115(2): 277-87, 2007 Jul.
Article in English | MEDLINE | ID: mdl-17592603

ABSTRACT

We constructed a 1,257-marker, high-density genetic map of Brassica oleracea spanning 703 cM in nine linkage groups, designated LG1-LG9. It was developed in an F2 segregating population of 143 individuals obtained by crossing double haploid plants of broccoli "Early-Big" and cauliflower "An-Nan Early". These markers are randomly distributed throughout the map, which includes a total of 1,062 genomic SRAP markers, 155 cDNA SRAP markers, 26 SSR markers, 3 broccoli BAC end sequences and 11 known Brassica genes: BoGSL-ALK, BoGSL-ELONG, BoGSL-PROa, BoGSL-PROb, BoCS-lyase, BoGS-OH, BoCYP79F1, BoS-GT (glucosinolate pathway), BoDM1 (resistance to downy mildew), BoCALa, BoAP1a (inflorescence architecture). BoDM1 and BoGSL-ELONG are linked on LG 2 at 0.8 cM, making it possible to use the glucosinolate gene as a marker for the disease resistance gene. By QTL analysis, we found three segments involved in curd formation in cauliflower. The map was aligned to the C genome linkage groups and chromosomes of B. oleracea and B. napus, and anchored to the physical map of A. thaliana. This map adds over 1,000 new markers to Brassica molecular tools.


Subject(s)
Brassica/genetics , Genetic Linkage , Arabidopsis/genetics , Chromosome Mapping , Genetic Markers , Genome, Plant , Phenotype , Quantitative Trait Loci
10.
Plant Cell Rep ; 25(6): 592-8, 2006 Jun.
Article in English | MEDLINE | ID: mdl-16432629

ABSTRACT

Gene BoGSL-PRO is associated with presence of 3-carbon side-chain glucosinolates (GSL). This gene is a member of the methylthioalkylmalate synthase (MAM) gene family. A BAC clone of Brassica oleracea, B21F5, containing this gene, was sequenced, annotated and compared to its corresponding region in Arabidopsis thaliana. Twelve protein-coding genes and 10 transposable elements were found in this clone. The corresponding region in A. thaliana chromosome I has 14 genes and no transposable elements. Analysis of MAM gene family in both species, which also include genes controlling 4-carbon side-chain GSL, separated the genes in two groups based on exon numbers and function. Phylogenetic analysis of the amino acid sequences encoded by these genes suggest that these two groups were produced by a duplication that must have occurred before the divergence of the Rosid and Asterid lineages of angiosperms. Comparison with putative orthologs from several prokaryotes further suggest that the members of the gene family with 10 exons, which encode proteins involved in 4-carbon side-chain GSL biosynthesis, were derived via truncation of the 3' end from ancestral genes more similar in length to those with 12 exons, which encode proteins involved in 3-carbon side-chain GSL biosynthesis. Lower gene density in B. oleracea compared to A. thaliana is due in part to presence of transposable elements (TE) mostly in inter-genic regions.


Subject(s)
Arabidopsis/enzymology , Brassica/enzymology , Oxo-Acid-Lyases/genetics , Phylogeny , Chromosomes, Artificial, Bacterial , Conserved Sequence , Gene Expression Regulation, Plant , Oxo-Acid-Lyases/metabolism , Sequence Analysis
11.
Theor Appl Genet ; 111(5): 949-55, 2005 Sep.
Article in English | MEDLINE | ID: mdl-16044267

ABSTRACT

We compared the sequence of a 96.7 Kb-long BAC clone (B 19 N 3) from Brassica oleracea (broccoli) with its corresponding regions in Arabidopsis thaliana. B 19 N 3 contains eight genes and 15 transposable elements (TEs). The first two genes in this clone, Bo 1 and Bo 2, have its corresponding region at the end of chromosome V of Arabidopsis (24 Mb). The third gene, Bo 3, corresponds to an ortholog at the opposite end (2.6 Mb) of the same chromosome. The other five genes, Bo 4 to Bo 8 also have a corresponding region on the same chromosome but at 7.7 Mb . These five genes are colinear with those found in the corresponding region of Arabidopsis, which contains, however, 15 genes. Therefore, a cluster of 10 genes is missing in B. oleracea clone (B 19 N 3). All five genes in common have the same order and orientation in the genomes of both species. Their 36 exons constituting the eight homologous genes have high conservation in size and sequence identity in both species. Among these, there is a major gene involved in aliphatic glucosinolate biosynthesis, Bo GSL-ELONG (Bo 4). Similar to A. thaliana, this gene, has a tandem duplicate, Bo 5. A contig for this region was constructed by primer walking and BAC-end-sequencing, revealing general gene colinearity between both species. During the 20 million years separating A. thaliana from B. oleracea from a common ancestor both genomes have diverged by chromosomal rearrangements and differential TE activity. These events, in addition to changes in chromosome number are responsible for the evolution of the genomes of both species. In spite of these changes, both species conserve general colinearity for their corresponding genes.


Subject(s)
Arabidopsis/genetics , Brassica/genetics , DNA Transposable Elements , Base Sequence , Chromosome Mapping , Chromosomes, Artificial, Bacterial , Cloning, Molecular , Expressed Sequence Tags , Gene Library , Reproducibility of Results
12.
Genome ; 47(4): 666-79, 2004 Aug.
Article in English | MEDLINE | ID: mdl-15284871

ABSTRACT

We compared the sequence of a 101-kb-long bacterial artificial chromosome (BAC) clone (B21H13) from Brassica oleracea with its homologous region in Arabidopsis thaliana. This clone contains a gene family involved in the synthesis of aliphatic glucosinolates. The A. thaliana homologs for this gene family are located on chromosome IV and correspond to three 2-oxoglutarate-dependent dioxygenase (AOP) genes. We found that B21H13 harbors 23 genes, whereas the equivalent region in Arabidopsis contains 37 genes. All 23 common genes have the same order and orientation in both Brassica and Arabidopsis. The 16 missing genes in the broccoli BAC clone were arranged in two major blocks of 5 and 7 contiguous genes, two singletons, and a twosome. The 118 exons comprising these 23 genes have high conservation between the two species. The arrangement of the AOP gene family in A. thaliana is as follows: AOP3 (GS-OHP) - AOP2 (GS-ALK) - pseudogene - AOP1. In contrast, in B. oleracea (broccoli and collard), two of the genes are duplicated and the third, AOP3, is missing. The remaining genes are arranged as follows: Bo-AOP2.1 (BoGSL-ALKa) - pseudogene - AOP2.2 (BoGSL-ALKb) - AOP1.1 - AOP1.2. When the survey was expanded to other Brassica accessions, we found variation in copy number and sequence for the Brassica AOP2 homologs. This study confirms that extensive rearrangements have taken place during the evolution of the Brassicacea at both gene and chromosomal levels.


Subject(s)
Brassica/genetics , Genes, Plant , Glucosinolates/genetics , Arabidopsis/genetics , Chromosomes, Artificial, Bacterial/genetics , Conserved Sequence , DNA, Plant/genetics , Evolution, Molecular , Exons , Gene Duplication , Phylogeny , Species Specificity
13.
Yi Chuan Xue Bao ; 29(8): 706-11, 2002.
Article in English | MEDLINE | ID: mdl-12200862

ABSTRACT

To detect quantitative trait loci (QTLs) controlling plant height, the plant height of 240 F2:3 lines derived from the cross of a dwarf wheat line ND3338 with a tall line F390, was assessed in field trials at two locations with three replications in 2000 and 2001. Microsatellite markers were used to construct a framework linkage map containing 215 loci with 21 linkage groups, and covering the whole genome about 3600cM. With the method of interval mapping, seven putative QTLs affecting plant height were detected on chromosomes 1B, 4B (two regions), 6A (two regions), 6D and 7A, respectively. Phenotypic variations explained by each QTL ranged from 5.2% to 50.1%, and in each environment the total putative QTLs explained about 64.8%-75% of the total phenotypic variation respectively. A major QTL located on chromosome arm 4BS near the locus Xgwm113, around the Rht-Blb locus, explained a large part of the phenotypic variation (27.8%-36.2% depending on the years or the locations). Except the QTL on chromosome 7A, all the other QTLs from ND3338 decreased the plant height, variously from 0.94 cm to 9.33 cm. Most of the identified QTLs were consistent in all the environments, and should be useful in future marker-assisted-selection programs for breeding dwarf and semi-dwarf wheat cultivars.


Subject(s)
Quantitative Trait, Heritable , Triticum/genetics , Chromosome Mapping , Crosses, Genetic , Microsatellite Repeats , Triticum/growth & development
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