scholarly journals Development of a New DNA Marker for Fusarium Yellows Resistance in Brassica rapa Vegetables

Plants ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 1082
Author(s):  
Naomi Miyaji ◽  
Mst Arjina Akter ◽  
Chizuko Suzukamo ◽  
Hasan Mehraj ◽  
Tomoe Shindo ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Amino Acid ◽  
Resistance Gene ◽  
Brassica Rapa ◽  
Dna Marker ◽  
Amino Acid Sequences ◽  
Inoculation Test ◽  
Causative Locus ◽  
Resistant Lines ◽  
Susceptible Allele

In vegetables of Brassica rapa L., Fusarium oxysporum f. sp. rapae (For) or F. oxysporum f. sp. conglutinans (Foc) cause Fusarium yellows. A resistance gene against Foc (FocBr1) has been identified, and deletion of this gene results in susceptibility (focbr1-1). In contrast, a resistance gene against For has not been identified. Inoculation tests showed that lines resistant to Foc were also resistant to For, and lines susceptible to Foc were susceptible to For. However, prediction of disease resistance by a dominant DNA marker on FocBr1 (Bra012688m) was not associated with disease resistance of For in some komatsuna lines using an inoculation test. QTL-seq using four F2 populations derived from For susceptible and resistant lines showed one causative locus on chromosome A03, which covers FocBr1. Comparison of the amino acid sequence of FocBr1 between susceptible and resistant alleles (FocBr1 and FocBo1) showed that six amino acid differences were specific to susceptible lines. The presence and absence of FocBr1 is consistent with For resistance in F2 populations. These results indicate that FocBr1 is essential for For resistance, and changed amino acid sequences result in susceptibility to For. This susceptible allele is termed focbr1-2, and a new DNA marker (focbr1-2m) for detection of the focbr1-2 allele was developed.

scholarly journals Identification and Mapping of Nucleotide Binding Site–Leucine-rich Repeat Resistance Gene Analogs in Bermudagrass

2010 ◽  
Vol 135 (1) ◽  
pp. 74-82 ◽  
Author(s):  
Karen R. Harris ◽  
Brian M. Schwartz ◽  
Andrew H. Paterson ◽  
Jeff A. Brady
Keyword(s):  
Disease Resistance ◽  
Amino Acid ◽  
Binding Site ◽  
Resistance Gene ◽  
Resistance Genes ◽  
Nucleotide Binding ◽  
Amino Acid Sequences ◽  
Resistance Gene Analogs ◽  
Leucine Rich Repeat ◽  
Linkage Groups

Thirty-one partial bermudagrass (Cynodon spp.) disease-resistance gene analogs (BRGA) were cloned and sequenced from diploid, triploid, tetraploid, and hexaploid bermudagrass using degenerate primers to target the nucleotide binding site (NBS) of the NBS–leucine-rich repeat (LRR) resistance gene family. Alignment of deduced amino acid sequences revealed that the conserved motifs of the NBS are present and all sequences have non-Drosophila melanogaster Toll and mammalian interleukin-1 receptor (TIR) motifs. Using a neighbor-joining algorithm, a dendrogram was created and nine groups of deduced amino acid sequences from bermudagrass could be identified from those sequences that span the NBS. Four BRGA markers and 15 bermudagrass expressed sequence tags (ESTs) with similarity to resistance genes or resistance gene analogs were placed on a bermudagrass genetic map. Multiple BRGA and EST markers mapped on T89 linkage groups 1a and 5a and clusters were seen on T89 19 and two linkage groups previously unidentified. In addition, three primers made from BRGA groups and ESTs with similarity to NBS-LRR resistance genes amplify NBS-LRR analogs in zoysiagrass (Zoysia japonica or Z. matrella) or seashore paspalum (Paspalum vaginatum). This gives evidence of conservation of NBS-LRR analogs among the subfamilies Chloridoideae and Panicoideae. Once disease resistance genes are identified, these BRGA and EST markers may be useful in marker-assisted selection for the improvement of disease resistance in bermudagrass.

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.

scholarly journals Characterization of a Bacteroides Mobilizable Transposon, NBU2, Which Carries a Functional Lincomycin Resistance Gene

2000 ◽  
Vol 182 (12) ◽  
pp. 3559-3571 ◽  
Author(s):  
Jun Wang ◽  
Nadja B. Shoemaker ◽  
Gui-Rong Wang ◽  
Abigail A. Salyers
Keyword(s):  
Amino Acid ◽  
Resistance Gene ◽  
Resistance Genes ◽  
Sequence Similarity ◽  
Antibiotic Resistance Genes ◽  
Small Region ◽  
Amino Acid Sequences ◽  
Integrase Gene ◽  
Site Specific ◽  
Lincomycin Resistance

ABSTRACT The mobilizable Bacteroides element NBU2 (11 kbp) was found originally in two Bacteroides clinical isolates,Bacteroides fragilis ERL and B. thetaiotaomicron DOT. At first, NBU2 appeared to be very similar to another mobilizable Bacteroides element, NBU1, in a 2.5-kbp internal region, but further examination of the full DNA sequence of NBU2 now reveals that the region of near identity between NBU1 and NBU2 is limited to this small region and that, outside this region, there is little sequence similarity between the two elements. The integrase gene of NBU2, intN2, was located at one end of the element. This gene was necessary and sufficient for the integration of NBU2. The integrase of NBU2 has the conserved amino acids (R-H-R-Y) in the C-terminal end that are found in members of the lambda family of site-specific integrases. This was also the only region in which the NBU1 and NBU2 integrases shared any similarity (28% amino acid sequence identity and 49% sequence similarity). Integration of NBU2 was site specific in Bacteroidesspecies. Integration occurred in two primary sites in B. thetaiotaomicron. Both of these sites were located in the 3′ end of a serine-tRNA gene NBU2 also integrated in Escherichia coli, but integration was much less site specific than inB. thetaiotaomicron. Analysis of the sequence of NBU2 revealed two potential antibiotic resistance genes. The amino acid sequences of the putative proteins encoded by these genes had similarity to resistances found in gram-positive bacteria. Only one of these genes was expressed in B. thetaiotaomicron, the homolog of linA, a lincomycin resistance gene fromStaphylococcus aureus. To determine how widespread elements related to NBU1 and NBU2 are in Bacteroides species, we screened 291 Bacteroides strains. Elements with some sequence similarity to NBU2 and NBU1 were widespread inBacteroides strains, and the presence oflinAN in Bacteroides strains was highly correlated with the presence of NBU2, suggesting that NBU2 has been responsible for the spread of this gene amongBacteroides strains. Our results suggest that the NBU-related elements form a large and heterogeneous family, whose members have similar integration mechanisms but have different target sites and differ in whether they carry resistance genes.

scholarly journals The Maintenance of Extreme Amino Acid Diversity at the Disease Resistance Gene, RPP13, in Arabidopsis thaliana

Genetics ◽  
2004 ◽  
Vol 166 (3) ◽  
pp. 1517-1527 ◽  
Author(s):  
Laura E. Rose ◽  
Peter D. Bittner-Eddy ◽  
Charles H. Langley ◽  
Eric B. Holub ◽  
Richard W. Michelmore ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Disease Resistance ◽  
Amino Acid ◽  
Resistance Gene ◽  
Disease Resistance Gene ◽  
Amino Acid Diversity

scholarly journals Characterization of Class 1 Integrons from Pseudomonas aeruginosa That Contain the blaVIM-2Carbapenem-Hydrolyzing β-Lactamase Gene and of Two Novel Aminoglycoside Resistance Gene Cassettes

2001 ◽  
Vol 45 (2) ◽  
pp. 546-552 ◽  
Author(s):  
Laurent Poirel ◽  
Thierry Lambert ◽  
Salih Türkoglü ◽  
Esthel Ronco ◽  
Jean-Louis Gaillard ◽  
...  
Keyword(s):  
Amino Acids ◽  
Pseudomonas Aeruginosa ◽  
Amino Acid ◽  
Resistance Gene ◽  
Gene Cassette ◽  
Amino Acid Sequences ◽  
Aminoglycoside Resistance ◽  
Class 1 Integron ◽  
Gene Cassettes ◽  
Class 1

ABSTRACT Two clonally unrelated Pseudomonas aeruginosa clinical strains, RON-1 and RON-2, were isolated in 1997 and 1998 from patients hospitalized in a suburb of Paris, France. Both isolates expressed the class B carbapenem-hydrolyzing β-lactamase VIM-2 previously identified in Marseilles in the French Riviera. In both isolates, thebla VIM-2 cassette was part of a class 1 integron that also encoded aminoglycoside-modifying enzymes. In one case, two novel aminoglycoside resistance gene cassettes,aacA29a and aacA29b, were located at the 5′ and 3′ end of the bla VIM-2 gene cassette, respectively. The aacA29a and aacA29b gene cassettes were fused upstream with a 101-bp part of the 5′ end of theqacE cassette. The deduced amino acid sequence AAC(6′)-29a protein shared 96% identity with AAC(6′)-29b but only 34% identity with the aacA7-encoded AAC(6′)-I1, the closest relative of the AAC(6′)-I family enzymes. These aminoglycoside acetyltransferases had amino acid sequences much shorter (131 amino acids) than the other AAC(6′)-I enzymes (144 to 153 amino acids). They conferred resistance to amikacin, isepamicin, kanamycin, and tobramycin but not to gentamicin, netilmicin, and sisomicin.

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