scholarly journals Identification of expressed resistance gene analogs (RGA) and development of RGA-SSR markers in tobacco

2015 ◽  
Vol 67 (2) ◽  
pp. 467-481 ◽  
Author(s):  
Qinghua Yuan ◽  
Ruihong Xie ◽  
Zhenchen Zhang ◽  
Zhuwen Ma ◽  
Jiqin Li ◽  
...  
Keyword(s):  
Resistance Gene ◽  
Pcr Amplification ◽  
Experimental System ◽  
Resistance Gene Analogs ◽  
R Genes ◽  
Data Set ◽  
The Public ◽  
Important Cash Crop ◽  
Plant Pathogen Interactions ◽  
Expressed Sequence

Tobacco is an important cash crop and an ideal experimental system for studies of plant-pathogen interactions. Identification of tobacco resistance (R) genes and resistance gene analogs (RGAs) is propitious to elucidate the underlying resistant mechanisms. In recent years, the public tobacco EST (expressed sequence tags) data set, which provides a rich source for identifying expressed RGAs, has enlarged substantially. In this study, 149606 Uni-ESTs were assembled from 412325 tobacco ESTs available in GenBank, scanned with 112 published plant R-genes protein sequences, and 1113 Nicotiana (tobacco) RGAs (NtRGAs) were identified. The majority of them comprised the common R-genes domains, such as NBS-LRR, LRR-PK, LRR, PK and Mlo, while we were unable to identify 109 RGAs using published domains of R-genes. Upon sequence alignment, 1079 NtRGAs were allocated on 712 loci within the Nicotiana benthamiana genome. A total of 78 simple sequence repeats (SSRs) were identified from 72 NtRGAs, and out of 64 newly designed primer pairs, 54 primer pairs generated clear bands upon PCR amplification using tobacco genomic DNA. Only nine primer pairs displayed polymorphism in 24 varieties of tobacco, with 2-4 alleles per locus (2.56 alleles on average), while 41 primer pairs were able to detect polymorphisms in six wild species of genus Nicotiana, with 2-4 alleles per locus (2.61 alleles on average).

Organization, Expression and Evolution of a Disease Resistance Gene Cluster in Soybean

Genetics ◽  
2002 ◽  
Vol 162 (4) ◽  
pp. 1961-1977
Author(s):  
Michelle A Graham ◽  
Laura Fredrick Marek ◽  
Randy C Shoemaker
Keyword(s):  
Disease Resistance ◽  
Resistance Gene ◽  
Resistance Genes ◽  
Developmental Stages ◽  
Gene Evolution ◽  
Pcr Amplification ◽  
Disease Resistance Genes ◽  
Disease Resistance Gene ◽  
R Genes ◽  
Specific Primers

Abstract PCR amplification was previously used to identify a cluster of resistance gene analogues (RGAs) on soybean linkage group J. Resistance to powdery mildew (Rmd-c), Phytophthora stem and root rot (Rps2), and an ineffective nodulation gene (Rj2) map within this cluster. BAC fingerprinting and RGA-specific primers were used to develop a contig of BAC clones spanning this region in cultivar “Williams 82” [rps2, Rmd (adult onset), rj2]. Two cDNAs with homology to the TIR/NBD/LRR family of R-genes have also been mapped to opposite ends of a BAC in the contig Gm_Isb001_091F11 (BAC 91F11). Sequence analyses of BAC 91F11 identified 16 different resistance-like gene (RLG) sequences with homology to the TIR/NBD/LRR family of disease resistance genes. Four of these RLGs represent two potentially novel classes of disease resistance genes: TIR/NBD domains fused inframe to a putative defense-related protein (NtPRp27-like) and TIR domains fused inframe to soybean calmodulin Ca2+-binding domains. RT-PCR analyses using gene-specific primers allowed us to monitor the expression of individual genes in different tissues and developmental stages. Three genes appeared to be constitutively expressed, while three were differentially expressed. Analyses of the R-genes within this BAC suggest that R-gene evolution in soybean is a complex and dynamic process.

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 Identification of Expressed Resistance Gene Analogs from Peanut (Arachis hypogaea L.) Expressed Sequence Tags

2013 ◽  
Vol 55 (5) ◽  
pp. 453-461 ◽  
Author(s):  
Zhanji Liu ◽  
Suping Feng ◽  
Manish K. Pandey ◽  
Xiaoping Chen ◽  
Albert K. Culbreath ◽  
...  
Keyword(s):  
Resistance Gene ◽  
Arachis Hypogaea ◽  
Expressed Sequence Tags ◽  
Resistance Gene Analogs ◽  
Arachis Hypogaea L ◽  
Expressed Sequence

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.

Electing the Senate

2017 ◽  
Author(s):  
Wendy J. Schiller ◽  
Charles Stewart III
Keyword(s):  
Original Data ◽  
State Legislators ◽  
Internal Conflict ◽  
Data Set ◽  
Senate Elections ◽  
Political Actors ◽  
The Public ◽  
Seventeenth Amendment ◽  
The People ◽  
Election Process

From 1789 to 1913, U.S. senators were not directly elected by the people—instead the Constitution mandated that they be chosen by state legislators. This radically changed in 1913, when the Seventeenth Amendment to the Constitution was ratified, giving the public a direct vote. This book investigates the electoral connections among constituents, state legislators, political parties, and U.S. senators during the age of indirect elections. The book finds that even though parties controlled the partisan affiliation of the winning candidate for Senate, they had much less control over the universe of candidates who competed for votes in Senate elections and the parties did not always succeed in resolving internal conflict among their rank and file. Party politics, money, and personal ambition dominated the election process, in a system originally designed to insulate the Senate from public pressure. The book uses an original data set of all the roll call votes cast by state legislators for U.S. senators from 1871 to 1913 and all state legislators who served during this time. Newspaper and biographical accounts uncover vivid stories of the political maneuvering, corruption, and partisanship—played out by elite political actors, from elected officials, to party machine bosses, to wealthy business owners—that dominated the indirect Senate elections process. The book raises important questions about the effectiveness of Constitutional reforms, such as the Seventeenth Amendment, that promised to produce a more responsive and accountable government.

Cloning and Analysis of NBS-LRR Type Disease Resistance Gene Analogs from Rosa rubus in Yunnan

2012 ◽  
Vol 34 (1) ◽  
pp. 56
Author(s):  
Ling CHEN ◽  
Hao ZHANG ◽  
Xian-Qin QIU ◽  
Hui-Jun YAN ◽  
Qi-Gang WANG ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Resistance Gene ◽  
Disease Resistance Gene ◽  
Resistance Gene Analogs

scholarly journals Clinical trial registries as Scientometric data: A novel solution for linking and deduplicating clinical trials from multiple registries

2021 ◽  
Author(s):  
Christian Thiele ◽  
Gerrit Hirschfeld ◽  
Ruth von Brachel
Keyword(s):  
Clinical Trials ◽  
Random Forest ◽  
Random Forest Model ◽  
Scientometric Analysis ◽  
Data Set ◽  
The Public ◽  
Forest Model ◽  
Clinical Trial Registries ◽  
Multiple Primary ◽  
Clinical Trials Registry

AbstractRegistries of clinical trials are a potential source for scientometric analysis of medical research and serve important functions for the research community and the public at large. Clinical trials that recruit patients in Germany are usually registered in the German Clinical Trials Register (DRKS) or in international registries such as ClinicalTrials.gov. Furthermore, the International Clinical Trials Registry Platform (ICTRP) aggregates trials from multiple primary registries. We queried the DRKS, ClinicalTrials.gov, and the ICTRP for trials with a recruiting location in Germany. Trials that were registered in multiple registries were linked using the primary and secondary identifiers and a Random Forest model based on various similarity metrics. We identified 35,912 trials that were conducted in Germany. The majority of the trials was registered in multiple databases. 32,106 trials were linked using primary IDs, 26 were linked using a Random Forest model, and 10,537 internal duplicates on ICTRP were identified using the Random Forest model after finding pairs with matching primary or secondary IDs. In cross-validation, the Random Forest increased the F1-score from 96.4% to 97.1% compared to a linkage based solely on secondary IDs on a manually labelled data set. 28% of all trials were registered in the German DRKS. 54% of the trials on ClinicalTrials.gov, 43% of the trials on the DRKS and 56% of the trials on the ICTRP were pre-registered. The ratio of pre-registered studies and the ratio of studies that are registered in the DRKS increased over time.

Characterization of nematode resistance gene analogs in tetraploid wheat

Plant Science ◽  
2003 ◽  
Vol 164 (1) ◽  
pp. 71-75 ◽  
Author(s):  
Maria Rosaria Cortese ◽  
Elena Fanelli ◽  
Carla De Giorgi
Keyword(s):  
Resistance Gene ◽  
Tetraploid Wheat ◽  
Nematode Resistance ◽  
Resistance Gene Analogs ◽  
Nematode Resistance Gene
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