Identification of resistance gene analogues (RGA) and development of E chromosome-specific RGA markers in wheat - Lophopyrum elongatum addition lines

2010 ◽  
Vol 61 (11) ◽  
pp. 929 ◽  
Author(s):  
Guo-Yue Chen ◽  
Yu-Ming Wei ◽  
Ya-Xi Liu ◽  
Li Wei ◽  
Ji-Rui Wang ◽  
...  
Keyword(s):  
Resistance Gene ◽  
Plant Disease Resistance ◽  
Evaluation Process ◽  
R Genes ◽  
Addition Lines ◽  
Degenerate Primers ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Lophopyrum Elongatum ◽  
Plant Resistance Gene

Degenerate primers designed from the conserved regions of nucleotide-binding site domains of known plant resistance gene products were used to scan a complete set of wheat–Lophopyrum elongatum addition lines. Forty-six clones were isolated and they were grouped into seven families of resistance gene analogues (RGA). All families were characterised as the Toll–Interleukin receptor group of R-genes (plant disease resistance genes). The putative chromosome-specific SNP (single-nucleotide polymorphism) loci were identified by multiple sequence alignments. Furthermore, 20 E chromosome-specific RGA markers were used to identify polymorphic fragments in wheat–Lo. elongatum addition lines and amphidiploid. The results suggested that these chromosome-specific markers could be not only useful for marker-assisted selection and map-based cloning of R-genes in Lo. elongatum, but also feasible for investigating the evaluation process of the E genome.

scholarly journals Identifying Resistance Gene Analogs Associated With Resistances to Different Pathogens in Common Bean

2003 ◽  
Vol 93 (1) ◽  
pp. 88-95 ◽  
Author(s):  
Camilo E. López ◽  
Iván F. Acosta ◽  
Carlos Jara ◽  
Fabio Pedraza ◽  
Eliana Gaitán-Solís ◽  
...  
Keyword(s):  
Common Bean ◽  
Resistance Gene ◽  
Plant Disease Resistance ◽  
Amino Acid Sequences ◽  
Yellow Mosaic Virus ◽  
Resistance Gene Analogs ◽  
R Genes ◽  
Degenerate Primers ◽  
Golden Yellow ◽  
Major Cluster

A polymerase chain reaction approach using degenerate primers that targeted the conserved domains of cloned plant disease resistance genes (R genes) was used to isolate a set of 15 resistance gene analogs (RGAs) from common bean (Phaseolus vulgaris). Eight different classes of RGAs were obtained from nucleotide binding site (NBS)-based primers and seven from not previously described Toll/Interleukin-1 receptor-like (TIR)-based primers. Putative amino acid sequences of RGAs were significantly similar to R genes and contained additional conserved motifs. The NBS-type RGAs were classified in two subgroups according to the expected final residue in the kinase-2 motif. Eleven RGAs were mapped at 19 loci on eight linkage groups of the common bean genetic map constructed at Centro Internacional de Agricultura Tropical. Genetic linkage was shown for eight RGAs with partial resistance to anthracnose, angular leaf spot (ALS) and Bean golden yellow mosaic virus (BGYMV). RGA1 and RGA2 were associated with resistance loci to anthracnose and BGYMV and were part of two clusters of R genes previously described. A new major cluster was detected by RGA7 and explained up to 63.9% of resistance to ALS and has a putative contribution to anthracnose resistance. These results show the usefulness of RGAs as candidate genes to detect and eventually isolate numerous R genes in common bean.

scholarly journals Greene SCPrimer: a rapid comprehensive tool for designing degenerate primers from multiple sequence alignments

2006 ◽  
Vol 34 (22) ◽  
pp. 6605-6611 ◽  
Author(s):  
Omar J. Jabado ◽  
Gustavo Palacios ◽  
Vishal Kapoor ◽  
Jeffrey Hui ◽  
Neil Renwick ◽  
...  
Keyword(s):  
Degenerate Primers ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Multiple Sequence Alignments

scholarly journals Isolation and Characterization of Nucleotide-Binding Site Resistance Gene Homologues in Common Bean (Phaseolus vulgaris)

2013 ◽  
Vol 103 (2) ◽  
pp. 156-168 ◽  
Author(s):  
Luz N. Garzón ◽  
Oscar A. Oliveros ◽  
Benjamin Rosen ◽  
Gustavo A. Ligarreto ◽  
Douglas R. Cook ◽  
...  
Keyword(s):  
Common Bean ◽  
Binding Site ◽  
Resistance Gene ◽  
Focal Point ◽  
Nucleotide Binding ◽  
Nucleotide Binding Site ◽  
R Genes ◽  
Degenerate Primers ◽  
Model Legume ◽  
Isolation And Characterization

Common bean production is constrained by many fungal, viral, and bacterial pathogens. Thus, the identification of resistance (R) genes is an important focal point of common bean research. The main goal of our study was to identify resistance gene homologues (RGH) in the crop, using degenerate primers designed from conserved sequences in the nucleotide-binding site (NBS) domains of R-genes from the model legume Medicago truncatula. Total DNA of the Andean common bean genotype G19833 was used for amplification of over 500 primer combinations. Sequencing of amplicons showed that 403 cloned fragments had uninterrupted open reading frames and were considered representative of functional RGH genes. The sequences were grouped at two levels of nucleotide identity (90 and 80%) and representative sequences of each group were used for phylogenetic analyses. The RGH sequence diversity of common bean was divided into TIR and non-TIR families, each with different clusters. The TIR sequences grouped into 14 clades while non-TIR sequences grouped into seven clades. Pairwise comparisons showed purifying selection, although some sequences may have been the result of diversifying selection. Knowledge about RGH genes in common bean can allow the design of molecular markers for pyramiding of resistance genes against various pathogens.

scholarly journals Isolation, Characterization and Phylogenetic Analysis of Nucleotide Binding Site-encoding Disease-resistance Gene Analogues from European Aspen (Populus tremula)

2010 ◽  
Vol 59 (1-6) ◽  
pp. 68-77 ◽  
Author(s):  
Yong Zhang ◽  
Shougong Zhang ◽  
Liwang Qi ◽  
Tao Zhang ◽  
Chunguo Wang ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Binding Site ◽  
Resistance Gene ◽  
Nucleotide Binding ◽  
Nucleotide Binding Site ◽  
Populus Tremula ◽  
R Gene ◽  
R Genes ◽  
Degenerate Primers ◽  
European Aspen

Abstract The majority of verified plant disease resistance genes (R genes) isolated to date was of the nucleotide binding site-leucine rich repeat (NBS-LRR) class. The conservation between different NBS-LRR R genes opens the avenue for the use of PCR based strategies in isolating and cloning other R gene family members or analogs (resistance gene analogue, RGA) using degenerate primers for these conserved regions. In this study, to better understand the R gene in European aspen (Populus tremula), a perennial tree, we used degenerate primers to amplify RGA sequences from European aspen. Cloning and sequence characterization identified 37 European aspen RGAs, which could be phylogenetically classified into seven subfamilies. Deduced amino acid sequences of European aspen RGAs showed strong identity, ranging from 30.41 to 46.63%, to toll interleukin receptor (TIR) R gene subfamily. BLAST searches with reference to the genomic sequence of P. trichocarpa found 209 highly homologous regions distributed in 28 genomic loci, suggesting the abundance and divergence of NBS-encoding R genes in European aspen genome. Although, numerous studies have reported that plant R genes are under diversifying selection for specificity to evolving pathogens, non-synonymous to synonymous nucleotide substitution (dN/dS) ratio were <1 for NBS domains of European aspen RGA, showing the evidence of purifying selection in this perennial tree. In further analysis, many intergenic exchanges were also detected among these RGAs, indicating a probable role in homogenising NBS domains. The present study permits insights into the origin, diversification, evolution and function of NBS-LRR R genes in perennial species like European aspen and will be useful for further R gene isolation and exploitation.

Isolation and linkage analysis of expressed disease-resistance gene analogues of sugar beet (Beta vulgaris L.)

Genome ◽  
2003 ◽  
Vol 46 (1) ◽  
pp. 70-82 ◽  
Author(s):  
Sandra Hunger ◽  
Gabriele Di Gaspero ◽  
Silke Möhring ◽  
Diana Bellin ◽  
Ralf Schäfer-Pregl ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Sugar Beet ◽  
Resistance Gene ◽  
Beta Vulgaris ◽  
Nematode Resistance ◽  
Kinase Domain ◽  
Disease Resistance Gene ◽  
R Genes ◽  
Degenerate Primers ◽  
Organ Specific

Sequence conservation among resistance genes (R genes) was exploited to identify 47 R gene analogues (RGAs) from sugar beet (Beta vulgaris L.). Using degenerate primers, 11 RGAs were amplified from genomic DNA and 7 from leaf or beet cDNA. Twenty-nine were selected from an EST sequencing program. Twenty-one RGAs contained structures similar to the nucleotide binding site (NBS) – leucine rich repeat (LRR) domain, a motif commonly found in several R genes. Among the remaining RGAs, 19 revealed similarity to the serine (threonine) protein kinase domain of R genes, 4 showed features related to the LRR region of the rice disease resistance gene Xa21, 1 RGA resembled the sugar beet nematode resistance gene Hs1pro-1, and 2 had homologies to other gene products associated with disease resistance. For 20 EST-derived RGAs, transcript levels were compared in leaf and root tissue revealing organ-specific transcription in 7 cases. Thirty-three RGAs were spread over all nine sugar beet chromosomes, except for a cluster of nine closely linked RGAs on chromosome 7. The analysis of linkage between RGAs and loci for rhizomania and Cercospora resistance identified alleles associated with resistance in both cases.Key words: RGA, Beta vulgaris, NBS–LRR, genetic linkage map, molecular marker.

scholarly journals Base-By-Base Version 3: New Comparative Tools for Large Virus Genomes

Viruses ◽  
2018 ◽  
Vol 10 (11) ◽  
pp. 637 ◽  
Author(s):  
Shin-Lin Tu ◽  
Jeannette Staheli ◽  
Colum McClay ◽  
Kathleen McLeod ◽  
Timothy Rose ◽  
...  
Keyword(s):  
Sequence Data ◽  
Degenerate Primers ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Multiple Sequence Alignments ◽  
Viral Genomes ◽  
User Data ◽  
Large Virus ◽  
Intuitive Interface ◽  
Virus Genomes

Base-By-Base is a comprehensive tool for the creation and editing of multiple sequence alignments that is coded in Java and runs on multiple platforms. It can be used with gene and protein sequences as well as with large viral genomes, which themselves can contain gene annotations. This report describes new features added to Base-By-Base over the last 7 years. The two most significant additions are: (1) The recoding and inclusion of “consensus-degenerate hybrid oligonucleotide primers” (CODEHOP), a popular tool for the design of degenerate primers from a multiple sequence alignment of proteins; and (2) the ability to perform fuzzy searches within the columns of sequence data in multiple sequence alignments to determine the distribution of sequence variants among the sequences. The intuitive interface focuses on the presentation of results in easily understood visualizations and providing the ability to annotate the sequences in a multiple alignment with analytic and user data.

Identification and characterization of NBS–LRR class resistance gene analogs in faba bean (Vicia faba L.) and chickpea (Cicer arietinum L.)

Genome ◽  
2006 ◽  
Vol 49 (10) ◽  
pp. 1227-1237 ◽  
Author(s):  
C. Palomino ◽  
Z. Satovic ◽  
J.I. Cubero ◽  
A.M. Torres
Keyword(s):  
Disease Resistance ◽  
Amino Acid ◽  
Resistance Gene ◽  
Vicia Faba ◽  
Cicer Arietinum ◽  
Faba Bean ◽  
Amino Acid Sequences ◽  
Resistance Gene Analogs ◽  
R Genes ◽  
Degenerate Primers

A PCR approach with degenerate primers designed from conserved NBS–LRR (nucleotide binding site – leucine-rich repeat) regions of known disease-resistance (R) genes was used to amplify and clone homologous sequences from 5 faba bean (Vicia faba) lines and 2 chickpea (Cicer arietinum) accessions. Sixty-nine sequenced clones showed homologies to various R genes deposited in the GenBank database. The presence of internal kinase-2 and kinase-3a motifs in all the sequences isolated confirm that these clones correspond to NBS-containing genes. Using an amino-acid sequence identitiy of 70% as a threshold value, the clones were grouped into 10 classes of resistance-gene analogs (RGA01 to RGA10). The number of clones per class varied from 1 to 30. RGA classes 1, 6, 8, and 9 were comprised solely of clones isolated from faba bean, whereas classes 2, 3, 4, 5, and 7 included only chickpea clones. RGA10, showing a within-class identity of 99%, was the only class consisting of both faba bean and chickpea clones. A phylogenetic tree, based on the deduced amino-acid sequences of 12 representative clones from the 10 RGA classes and the NBS domains of 6 known R genes (I2 and Prf from tomato, RPP13 from Arabidopsis, Gro1–4 from potato, N from tobacco, L6 from flax), clearly indicated the separation between TIR (Toll/interleukin-1 receptor homology: Gro1–4, L6, N, RGA05 to RGA10)- and non-TIR (I2, Prf, RPP13, RGA01 to RGA04)-type NBS–LRR sequences. The development of suitable polymorphic markers based on cloned RGA sequences to be used in genetic mapping will facilitate the assessment of their potential linkage relationships with disease-resistance genes in faba bean and chickpea. This work is the first to report on faba bean RGAs.

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