scholarly journals Genetic Variation Among Isolates of the Web Blight Pathogen of Common Bean Based on PCR-RFLP of the ITS-rDNA Region

Plant Disease ◽  
2003 ◽  
Vol 87 (7) ◽  
pp. 766-771 ◽  
Author(s):  
G. Godoy-Lutz ◽  
J. R. Steadman ◽  
B. Higgins ◽  
K. Powers
Keyword(s):  
Common Bean ◽  
Management Practices ◽  
Rflp Analysis ◽  
Enzymatic Digestion ◽  
Nuclear Ribosomal Dna ◽  
5.8S Rdna ◽  
Dna Repeat ◽  
Pcr Rflp ◽  
Polymerase Chain ◽  
Web Blight

Variability of 45 isolates of Rhizoctonia solani (teleomorph Thanatephorus cucumeris) causing web blight (WB) of common bean, Phaseolus vulgaris, was examined by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis of the internal transcribed spacer regions (ITS1 and ITS2) and the 5.8S subunit (5.8S) of the nuclear ribosomal DNA repeat (ITS-5.8S-rDNA). Isolates were collected from diseased bean leaves from Argentina, Costa Rica, Cuba, Dominican Republic, Honduras, Panama, and Puerto Rico. These WB isolates belong to AG-1 and AG-2 based on anastomosis reaction. Isolates of AG-1 that cause WB were separated into three distinct groups of RFLP patterns from enzymatic digestion of a 740-bp PCR fragment. Microsclerotia-producing isolates (<1 mm) were differentiated from macrosclerotia-producing isolates (5 to 20 mm) based on PCR-RFLP patterns even though they are placed in the same AG1-1B subgroup by anastomosis reaction. WB isolates of AG-2 were separated into two distinct PCR-RFLP groups as previously reported. AG-1 macrosclerotial-producing isolates were the most virulent, whereas isolates of AG-2 were the least virulent. Genetic variability of the WB pathogen may have influenced the failure or success of management practices implemented in the past in Latin America.

scholarly journals Genetic Sequence Variation in the ITS Region of Nine Rubus Genotypes

HortScience ◽  
2004 ◽  
Vol 39 (4) ◽  
pp. 754A-754 ◽  
Author(s):  
Eric Stafne* ◽  
John Clark ◽  
Allen Szalanski
Keyword(s):  
Genetic Variation ◽  
Rflp Analysis ◽  
Small Variation ◽  
Its Region ◽  
Genetic Distances ◽  
Nuclear Ribosomal Dna ◽  
Internal Transcribed Spacer Region ◽  
Pcr Rflp ◽  
Restriction Sites ◽  
Polymerase Chain

In this study, the nuclear ribosomal DNA internal transcribed spacer region (ITS) of six Rubus cultivars were sequenced, then compared with sequences of three Rubus species in Genbank. DNA sequencing revealed little genetic variation among blackberry cultivars, but ably revealed distinctions between blackberry and red raspberry genotypes. Analysis by maximum-parsimony and pairwise genetic distances confirmed the small variation among blackberry cultivars. The resulting sequences were analyzed for useful restriction sites and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis was conducted on a total of six cultivars to establish genetic variation. Digests were difficult to interpret due to heterogeneity at restriction sites.

Genetic diversity among a complex of cereal cyst nematodes inferred from RFLP analysis of the ribosomal internal transcribed spacer region

Genome ◽  
1997 ◽  
Vol 40 (4) ◽  
pp. 479-486 ◽  
Author(s):  
S. Bekal ◽  
J. P. Gauthier ◽  
R. Rivoal
Keyword(s):  
Phylogenetic Relationships ◽  
Internal Transcribed Spacer ◽  
Rflp Analysis ◽  
Restriction Pattern ◽  
Nuclear Ribosomal Dna ◽  
Heterodera Avenae ◽  
Cyst Nematodes ◽  
Internal Transcribed Spacer Region ◽  
5.8S Rdna ◽  
Pcr Rflp

This study examined the restriction polymorphism (RFLP) of the nuclear ribosomal DNA in Heterodera avenae, H. filipjevi, H. mani, H. latipons, and the taxonomically unclear Gotland strain in order to establish a molecular characterization and phylogenetic relationships in the complex of cereal cyst nematodes (CCN). The internal transcribed spacer (ITS) and 5.8S rDNA were amplified by PCR from a single female or a cyst of 27 different geographic isolates of the CCN complex and one population of H. schachtii, used as outgroup. The amplified product was 1.2 kb long and 14 of 15 enzymes produced restriction fragments for each isolate. Relationships between populations were determined from UPGMA analysis based on distance values calculated from RFLP data. Digestions with TaqI clearly differentiated H. avenae, H. latipons, and a group composed of H. filipjevi and the Gotland strain. Six endonucleases (HaeIII, HinfI, ItaI, PstI, TaqI, and Tru9I) produced the same restriction pattern with H. filipjevi and the Gotland strain, and both were clearly separated from H. avenae with PstI. Restriction sites have revealed a mixture of the species H. latipons and H. avenae, and possible infraspecific variation in H. avenae. The inferred phylogenetic relationships of species in the CCN complex are in agreement with their morphological characterization.Key words: cereal cyst nematodes, Heterodera avenae, PCR, RFLP, ribosomal diversity.

scholarly journals Association of growth hormone (GH) gene polymorphism with growth and carcass in Sumba Ongole (SO) cattle

2017 ◽  
Vol 42 (3) ◽  
pp. 153 ◽  
Author(s):  
P. P. Agung ◽  
S. Anwar ◽  
W. P. B. Putra ◽  
M. S. A. Zein ◽  
A. S. Wulandari ◽  
...  
Keyword(s):  
Growth Hormone ◽  
Gene Polymorphism ◽  
Fragment Length Polymorphism ◽  
Growth Parameters ◽  
Rflp Analysis ◽  
Cattle Breeding ◽  
Pcr Rflp ◽  
Gh Gene ◽  
Polymerase Chain ◽  
Dressing Percentage

A study was conducted to identify the polymorphism in the intron 3 of the Growth Hormone (GH) gene and also to evaluate the association of the GH gene polymorphism with growth parameters and dressing percentage in the Sumba Ongole (SO) cattle. A total of 267 individual DNA samples were used in the Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) analysis. The SO cattle growth parameters data (n=44) including birth weight (BW), weaning weight at 205 days of age (WW205), yearling weight at 365 days of age (YW365) and also dressing percentage (DP) (n=122) were investigated in this study. There were three genotypes (AA, AB, and BB) of the GH gene based on the PCR-RFLP analysis with allele frequency was 0.87 and 0.13 for A allele and B allele respectively. The highest genotype frequency in the SO cattle is AA (0.76) and the lowest is BB (0.02). The Heterozygosity Observed (Ho) value in the SO cattle population is 0.23 and Polymorphism Information Content (PIC) value is 0.20. Therefore, the genetic diversity in the SO cattle based on the GH gene polymorphism is quite low. There is no association (P>0.05) in BW, WW205, YW365, and DP with genotypes of the GH gene. As the result, the GH gene in this study cannot be used as a genetic marker in the SO cattle breeding program.

scholarly journals MMP-7 A-181G Polymorphism in Breast Cancer Patients from Western Iran

Breast Care ◽  
2015 ◽  
Vol 10 (6) ◽  
pp. 398-402 ◽  
Author(s):  
Kheirollah Yari ◽  
Ziba Rahimi ◽  
Mehrdad Payandeh ◽  
Zohreh Rahimi
Keyword(s):  
Breast Cancer ◽  
Cancer Patients ◽  
Fragment Length Polymorphism ◽  
Ductal Carcinoma ◽  
Lobular Carcinoma ◽  
Rflp Analysis ◽  
Breast Cancer Patients ◽  
Western Iran ◽  
Pcr Rflp ◽  
Polymerase Chain

Background: Matrix metalloproteinases (MMPs) are upregulated in tumors. The MMP-7 A-181G polymorphism is associated with increased expression of the MMP-7 gene. Aim of the present study was to investigate the association between the MMP-7 A-181G polymorphism and susceptibility to breast cancer. Patients and Methods: The MMP-7 A-181G variants were studied in a cohort of 251 subjects consisting of 100 breast cancer patients and 151 healthy controls; all were from Western Iran. The MMP-7 A-181G genotypes were identified using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis. Results: The frequencies of the MMP-7 AA, AG, and GG genotypes in healthy individuals were 34.4, 50.4, and 15.2%, respectively. In breast cancer patients, the frequencies of AA (34%), AG (52%), and GG (14%) genotypes (p = 0.95) were similar to those in the controls. There was a trend toward an increased frequency of the combined genotype of MMP-7 AG+GG in patients with lymph node metastasis (70.4%) compared to those without metastasis (66.7%). Also, in patients with invasive lobular carcinoma, the frequency of the MMP-7 AG+GG genotype tended to be higher (71.4%) compared to that in patients with invasive ductal carcinoma (66.2%) (p = 0.78). Conclusion: Our findings indicate that the MMP-7 A-181G polymorphism may not be correlated with susceptibility to breast cancer in our population.

scholarly journals Molecular Detection of Toxoplasma gondii and Neospora caninum in Domestic Ducks in Hunan Province, China

2021 ◽  
Vol 8 ◽  
Author(s):  
Qiu-Yan Lv ◽  
He-Liang Zheng ◽  
Wen-He Yang ◽  
Guo-Hua Liu
Keyword(s):  
Toxoplasma Gondii ◽  
Neospora Caninum ◽  
Rflp Analysis ◽  
Hunan Province ◽  
Economic Losses ◽  
Domestic Ducks ◽  
New Information ◽  
B1 Gene ◽  
Pcr Rflp ◽  
Polymerase Chain

Toxoplasma gondii and Neospora caninum are protozoan parasites that infect warm-blooded animals, and cause major economic losses in livestock industries worldwide. However, little is known about the genotypes of T. gondii and N. caninum in domestic ducks in China. Herein, brain samples from 588 domestic ducks from Hunan province in China were examined for the presence of T. gondii and N. caninum. Polymerase chain reaction (PCR) was used to detect T. gondii B1 gene and N. caninum NC-5 gene. Forty-five DNA samples (7.7%; 95% CI: 5.5–9.9) were positive for B1 gene, and two (0.3%; 95% CI: 0–0.7) were positive for NC-5 gene. The risk factors significantly associated with T. gondii infection were age and sex. The 45 samples positive for T. gondii were genotyped using multi-locus PCR-RFLP analysis and only one sample was fully genotyped as ToxoDB#9 (Chinese I). These results provide new information about the epidemiology of T. gondii and N. caninum in ducks in Hunan province in China. The data also highlight the importance of a “One Health” approach to dealing with toxoplasmosis.

scholarly journals Molecular Detection and PCR-RFLP Analysis of Mucoviscosity-Associated Gene A (magA) in Clinical Isolates of Multidrug-Resistant Klebsiella pneumoniae in Bangladesh

2020 ◽  
Vol 14 (1) ◽  
pp. 196-204
Author(s):  
Md. Hazrat Ali ◽  
Saeed Anwar ◽  
Nusrat Jahan Toma ◽  
Ikram Rafid ◽  
Md. Kamrul Hasan ◽  
...  
Keyword(s):  
Molecular Detection ◽  
Clinical Specimen ◽  
Rflp Analysis ◽  
Multidrug Resistant ◽  
Clinical Isolates ◽  
Specific Gene ◽  
Multicenter Cohort ◽  
Pcr Rflp ◽  
Invasive Infections ◽  
Polymerase Chain

Background and Objective: The mucoviscosity associated gene A (magA) in the hypermucoviscous variants of K. pneumoniae is reported to be associated with invasive infections and considered a virulence factor. We sought to analyze the magA genes in K. pneumoniae isolates in the clinical specimen collected from Bangladesh. Methods: We established a multicenter cohort of patients with Klebsiella infection hospitalized at 05 different hospitals between September 2016 and April 2017. We collected 313 K. pneumoniae isolates from patients who consented to participate in the study. The isolates were evaluated for harboring the magA genes using a single-tube multiplexed polymerase chain reaction. The magA genes were analyzed by PCR-RFLP technique using two enzymes, namely PciI and SmaI. Antibiogram assay using 12 commercially available antibiotic discs was performed on all the isolates. Results: The presence of K. pneumoniae specific gene (ureD) was confirmed in all the isolates. The percentage of isolates harboring the magA gene was 7.34%(23 isolates), the majority of which was collected from the patients admitted in intensive care units (16 isolates, 69.6%), and infectious diseases wards (5 isolates, 21.7%). PCR-RFLP analysis revealed that for 7 out of 23 isolates, where Sma1 could not cleave the magA gene. All the isolates showed resistance to ampicillin, carbenicillin cefradine, chloramphenicol, erythromycin, kanamycin, and sulphamethoxazole, though the extent was varying. However, imipenem showed 100% sensitivity to all the tested isolates. Conclusion: This study demonstrates the presence of the magA gene in multidrug-resistant clinical isolates of K. pneumoniae collected from Bangladesh.

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