scholarly journals Polymorphism, Allelic and Genotypic Frequencies of κ-Casein and β-LG genes in Egyptian Buffaloes

2020 ◽  
Vol 12 (4) ◽  
pp. 283
Author(s):  
Z. M. Al-Shawa ◽  
M. F. El-Zarei ◽  
A. A. Ghazy ◽  
M. A. Ayoub ◽  
S. M. Merdan ◽  
...  
Keyword(s):  
Genetic Parameters ◽  
Rflp Analysis ◽  
Restriction Enzymes ◽  
Pcr Product ◽  
Heterozygosity Excess ◽  
Pcr Rflp ◽  
Native Populations ◽  
Egyptian Buffalo ◽  
Rflp Assay ◽  
Geographical Locations

With a view to detecting the genotypes of both κ-CN and β-LG genes in native populations of Egyptian buffalo using PCR-RFLP technique, 80 randomly, individuals were selected from five geographical locations of some Egyptian provinces. Also, to estimate the population genetic parameters such as, allelic and genotypic frequencies, heterozygosity, and inbreeding coefficient (FIS) of these studied genes. For genotyping, 453 bp PCR product of κ-CN was digested with AcuI and HpyCH4IV (Isoschizomer for MaeII) restriction enzymes while the 247 bp PCR product of β-LG was digested with HaeIII restriction enzyme. PCR-RFLP results discovered polymorphism at the level of κ-CN gene in all studied Egyptian buffaloes with two distinct alleles “A” and “B”. PCR-RFLP analysis for κ-CN gene using both restriction enzymes successfully detected that polymorphic status of the studied populations. We recommended using AcuI enzyme which was more capable for differentiating between homozygous (17%) and heterozygous (83%) individuals than HpyCH4IV enzyme which defined only 4% of homozygous individuals and the remaining was heterozygous (96%) individuals. Existence of heterozygosity excess in all studied populations referred to higher degree of genetic variability between individuals within these populations. On contrary, results of PCR-RFLP at the level of β-LG gene revealed a monomorphic pattern of Egyptian buffaloes and genotyped as “AA” animals which signified that PCR-RFLP assay with HaeIII enzyme for β-LG gene failed to discover any evidence of polymorphism in Egyptian buffalo under the circumstances of this study or all studied animals possess only one allele.

scholarly journals Identification and differentiation among chicken’s, duck’s, quail’s, rabbit’s and turkey's meat using PCR-RFLP technique

2015 ◽  
Vol 31 (1) ◽  
pp. 101-108 ◽  
Author(s):  
S.M. Abdel-Rahman ◽  
A.M. Elmaghraby ◽  
A.S. Haggag
Keyword(s):  
Mitochondrial Dna ◽  
Cytochrome B ◽  
Fragment Length ◽  
Restriction Analysis ◽  
Restriction Enzymes ◽  
Pcr Product ◽  
Pcr Rflp ◽  
Pcr Products ◽  
Species Specific ◽  
Rflp Assay

PCR-RFLP technique was developed for identification and differentiation among chicken?s, duck?s, quail?s, rabbit?s and turkey's meat. DNA from small amount of muscles (0.05 g) was extracted and a region of mitochondrial DNA (cytochrome-b gene) in chicken, duck, quail, rabbit and turkey was amplified by PCR. Fragment length of the PCR product was 371 bp in chicken, 374 bp in duck and rabbit and 377 bp in both quail and turkey. Six nucleotides different makes it difficult to differentiate among these five species-specific meat. For differentiation, three different restriction enzymes (DdeI, MspI and TaqI) were used to digest the PCR products. Restriction analysis showed difference among chicken?s, duck?s, quail?s, rabbit?s and turkey's meat. Where, DdeI yielded two fragments (291 and 83 bp) only in rabbit?s meat. MspI yielded three fragments (221, 85 and 65 bp) in chicken?s meat and two fragments (290 and 87 bp) in both quail?s and turkey's meat. TaqI yielded three fragments (146, 134 and 94 bp) in duck?s meat and two fragments (226 and 151 bp) in quail?s meat. The use of Cytb- PCR-RFLP assay allowed a direct and fast authentication and differentiation among chicken?s, duck?s, quail?s, rabbit?s and turkey's meat.

scholarly journals Identification of Pneumococcal Serotypes by PCR–Restriction Fragment Length Polymorphism

Diagnostics ◽  
2019 ◽  
Vol 9 (4) ◽  
pp. 196 ◽  
Author(s):  
García-Suárez ◽  
González-Rodríguez ◽  
Cima-Cabal ◽  
Yuste ◽  
Vazquez ◽  
...  
Keyword(s):  
Restriction Fragment Length Polymorphism ◽  
Restriction Fragment ◽  
Length Polymorphism ◽  
Dna Sequences ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Rflp Analysis ◽  
Restriction Enzymes ◽  
Pcr Rflp ◽  
Restriction Fragment Length

Streptococcus pneumoniae shows more than 90 capsular serotypes that can be distinguished by their reactivity against antisera. The main objective of this work was the development of a molecular method for serotyping without the use of antisera. A computer program containing an algorithm was used to search in a database for potentially useful enzymes for Restriction Fragment Length Polymorphism-RFLP typing, in order to maximize the discrimination between different serotypes. DNA sequences of 90 serotypes for the region between dexB and aliA genes were compiled, and a computer screening of restriction enzymes was performed. The wzg–wzh–wzd–wze region and Sse9I restriction predicted unique PCR-RFLP patterns for 39 serotypes and eight serogroups. A second restriction enzyme resolved fragment specific patterns for 25 serotypes. The method was tested with 98 serotype-unknown clinical isolates. PCR-RFLP analysis deduced correct serotypes that were confirmed by Quellung reaction for 78.5% of the isolates.

PCR-based genetic identification of marlin and other billfish

1998 ◽  
Vol 49 (5) ◽  
pp. 383 ◽  
Author(s):  
B. H. Innes ◽  
P. M. Grewe ◽  
R. D. Ward
Keyword(s):  
Mitochondrial Dna ◽  
Genetic Test ◽  
Rflp Analysis ◽  
Restriction Enzymes ◽  
Genetic Identification ◽  
Dna Molecule ◽  
Pcr Rflp ◽  
D Loop ◽  
Specific Variation ◽  
Species Specific

A genetic test was developed for the identification of the six species of billfish found in Australian waters (black marlin, Indo–Pacific blue marlin, striped marlin, Indo–Pacific sailfish, shortbill spearfish and broadbill swordfish). The test was based on the PCR–RFLP analysis of a 1400 bp region of the mitochondrial DNA molecule, the d-loop, using four restriction enzymes (Hinf I, Rsa I and Sau3A I andTaq I). A total of 33 composite haplotypes were observed among 160 fish; all were species-specific. Three of the species—black marlin, striped marlin and broadbill swordfish—showed sufficient intra-specific variation to be useful in population structure analyses.

PCR–RFLP analysis of mitochondrial DNA for identification of Rutilus rutilus caspicus populations on the southern coast of the Caspian Sea, Iran

2006 ◽  
Vol 86 (6) ◽  
pp. 1463-1467 ◽  
Author(s):  
Sohrab Rezvani ◽  
Amin Eimanifar ◽  
Reza Aghili ◽  
Faramarz Laloei
Keyword(s):  
Caspian Sea ◽  
Rflp Analysis ◽  
Restriction Enzymes ◽  
Rutilus Rutilus ◽  
Southern Coast ◽  
The Caspian Sea ◽  
Length Polymorphisms ◽  
Pcr Rflp ◽  
Nucleotide Divergence ◽  
Genetic Pools

Genetic analysis using restriction fragment length polymorphisms (RFLPs) of cytochrome b in mtDNA was made to clarify genetic variations among two Iranian Rutilus rutilus caspicus populations of commercial importance from the southern coast of the Caspian Sea. Polymorphism was detected using six restriction enzymes and a total of six composite haplotypes were identified. Four haplotypes were rare occurring only once in two regions (west and east of the southern Caspian Sea). Nucleotide and haplotype diversities were higher in the south-west region of the Caspian Sea (π=3.43%, h=23.3).The nucleotide divergence between the two populations was low (0.064%). The test for heterogeneity of composite haplotype frequencies gave no significant outcome for all samples (χ2=0.137, P≤0.05). The results indicate that significant attention should be paid to the genetic characterization of R. rutilus caspicus populations for conservation of their genetic pools and aquaculture policies at the coastlines of the Caspian Sea.

scholarly journals Detection and characterization of Leptospira spp. isolated from aborted bovine clinical samples

2011 ◽  
Vol 81 (1) ◽  
pp. 21-25 ◽  
Author(s):  
Hassan Momtaz ◽  
Saadat Moshkelani
Keyword(s):  
Public Health Problem ◽  
Rflp Analysis ◽  
Restriction Enzymes ◽  
Clinical Samples ◽  
Dairy Herds ◽  
Important Public Health Problem ◽  
Pcr Rflp ◽  
Beef Herds ◽  
Bovine Abortion

Leptospira is recognized as an important public health problem worldwide, especially in tropical countries, and is a common cause of abortion in dairy and beef herds. The aim of the present study was to detect and characterize Leptospira as the causative agent of abortion in cattle using a PCR-RFLP in Chaharmahal va Bakhtiari and Isfahan provinces, Iran. A total of 220 bovine aborted foetuses and 120 vaginal discharges from an aborted calf were collected from 64 commercial dairy herds. After isolation of 60 Leptospira spp. from samples, RFLP analysis was carried out with HindIII and HaeIII restriction enzymes in reference strains and isolated for characterization. In a total of 340 specimens, 46 (20.9%) and 14 (11.66%) were identified positive for Leptospira spp. from aborted bovine foetuses and vaginal discharges, respectively. The present results also suggest that L. interrogans serovar hardjo has the highest prevalence in the region under study and L. hardjo is a major pathogen causing bovine abortion in Chaharmahal va Bakhtiari and Isfahan provinces of Iran.

scholarly journals PHYLOGENETIC RELATIONSHIPS AMONGST 10 Durio SPECIES BASED ON PCR-RFLP ANALYSIS OF TWO CHLOROPLAST GENES

2013 ◽  
Vol 6 (1) ◽  
pp. 20 ◽  
Author(s):  
Panca J. Santoso ◽  
Ghizan B. Saleh ◽  
Norihan M. Saleh ◽  
Suhaimi Napis
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Relationships ◽  
Rflp Analysis ◽  
Restriction Enzymes ◽  
Rbcl Gene ◽  
Research Station ◽  
Taxonomic Level ◽  
Pcr Rflp ◽  
Young Leaves ◽  
Reliable Marker

Twenty seven species of Durio have been identified in Sabah and Sarawak, Malaysia, but their relationships have not been studied. This study was conducted to analyse phylogenetic relationships amongst 10 Durio species in Malaysia using PCR-RFLP on two chloroplast DNA genes, i.e. ndhC-trnV and rbcL. DNAs were extracted from young leaves of 11 accessions from 10 Durio species collected from the Tenom Agriculture Research Station, Sabah, and University Agriculture Park, Universiti Putra Malaysia. Two pairs of oligonucleotide primers, N1-N2 and rbcL1-rbcL2, were used to flank the target regions ndhC-trnV and rbcL. Eight restriction enzymes, HindIII, BsuRI, PstI, TaqI, MspI, SmaI, BshNI, and EcoR130I, were used to digest the amplicons. Based on the results of PCR-RFLP on ndhC-trnV gene, the 10 Durio species were grouped into five distinct clusters, and the accessions generally showed high variations. However, based on the results of PCR-RFLP on the rbcL gene, the species were grouped into three distinct clusters, and generally showed low variations. This means that ndhC-trnV gene is more reliable for phylogenetic analysis in lower taxonomic level of Durio species or for diversity analysis, while rbcL gene is reliable marker for phylogenetic analysis at higher taxonomic level. PCR-RFLP on the ndhC-trnV and rbcL genes could therefore be considered as useful markers to phylogenetic analysis amongst Durio species. These finding might be used for further molecular marker assisted in Durio breeding program.

Genetic Polymorphisms of Chicken Antiviral Mx1 and TVB Genes in Indigenous and Giriraja Chicken

2021 ◽  
Author(s):  
S. Nihar ◽  
S. Naveen Kumar ◽  
Wilfred Ruban ◽  
H.M. Yathish ◽  
R. Nagaraja ◽  
...  
Keyword(s):  
Restriction Enzyme ◽  
Dna Isolation ◽  
Pcr Amplification ◽  
Rflp Analysis ◽  
Isoamyl Alcohol ◽  
Gene Frequencies ◽  
Pcr Product ◽  
Pcr Rflp ◽  
Recent Developments ◽  
Mx1 Gene

Background: Recent developments in molecular genetics lead to addressing certain poultry diseases via breeding for disease resistance. The present study was carried to identify and compare the genetic polymorphism in Chicken Mx1 and TVB genes among the indigenous and Giriraja chicken using PCR-RFLP technique. Methods: Blood samples were collected from 50 indigenous and 50 Giriraja birds and DNA isolation was done by Phenol: Chloroform: Isoamyl alcohol method. PCR amplification of Chicken Mx1 (exon 14) and Chicken TVB (exon 3) genes was carried out followed by RFLP analysis. Result: PCR product sizes of 301 bp and 303 bp of Mx1 and TVB genes, respectively were successfully amplified. RFLP analysis of Mx1 gene with Hyp8I restriction enzyme revealed three genotypes AA, AB and BB. In indigenous birds genotypic frequencies of AA, AB and BB were 0.314, 0.493 and 0.194, respectively and gene frequencies were 0.56 and 0.44 for alleles A and B, respectively. In Giriraja birds, genotypic frequencies for AA, AB and BB were 0.27, 0.499 and 0.23, respectively and gene frequencies were 0.52 and 0.48 for alleles A and B, respectively. RFLP analysis of TVB gene with NlaIII restriction enzyme revealed two genotypes viz., AA and AB. In indigenous birds genotypic frequencies of AA and AB were 0.81 and 0.18, respectively and gene frequencies were 0.9 and 0.1 for alleles A and B, respectively. In Giriraja birds genotypic frequencies for AA and AB were 0.774 and 0.211, respectively and gene frequencies were 0.88 and 0.12 for alleles A and B, respectively.

scholarly journals Rapid differentiation of Staphylococcus aureus isolates harbouring egc loci with pseudogenes ψent1 and ψent2 and the selu or selu v gene using PCR-RFLP

2007 ◽  
Vol 56 (2) ◽  
pp. 208-216 ◽  
Author(s):  
Mark M. Collery ◽  
Cyril J. Smyth
Keyword(s):  
Dna Sequencing ◽  
Restriction Enzyme ◽  
Sequence Similarity ◽  
Rflp Analysis ◽  
Restriction Enzymes ◽  
Restriction Enzyme Digestion ◽  
Pcr Rflp ◽  
Intergenic Regions ◽  
Unique Restriction ◽  
Genomic Regions

The egc locus of Staphylococus aureus harbours two enterotoxin genes (seg and sei) and three enterotoxin-like genes (selm, seln and selo). Between the sei and seln genes are located two pseudogenes, ψent1 and ψent2, or the selu or selu v gene. While these two alternative sei–seln intergenic regions can be distinguished by PCR, to date, DNA sequencing has been the only confirmatory option because of the very high degree of sequence similarity between egc loci bearing the pseudogenes and the selu or selu v gene. In silico restriction enzyme digestion of genomic regions encompassing the egc locus from the 3′ end of the sei gene through the 5′ first quarter of the seln gene allowed pseudogene- and selu- or selu v-bearing egc loci to be distinguished by PCR-RFLP. Experimental application of these findings demonstrated that endonuclease HindIII cleaved PCR amplimers bearing pseudogenes but not those with a selu or selu v gene, while selu- or selu v-bearing amplimers were susceptible to cleavage by endonuclease HphI, but not by endonuclease HindIII. The restriction enzyme BccI cleaved selu- or selu v-harbouring amplimers at a unique restriction site created by their signature 15 bp insertion compared with pseudogene-bearing amplimers, thereby allowing distinction of these egc loci. PCR-RFLP analysis using these restriction enzymes provides a rapid, easy to interpret alternative to DNA sequencing for verification of PCR findings on the nature of an egc locus type, and can also be used for the primary identification of the intergenic sei–seln egc locus type.

Rapid identification of Amaranthus caudatus and Amaranthus hypochondriacus by sequencing and PCR–RFLP analysis of two starch synthase genes

Genome ◽  
2012 ◽  
Vol 55 (8) ◽  
pp. 623-628 ◽  
Author(s):  
Young-Jun Park ◽  
Tomotaro Nishikawa
Keyword(s):  
Rflp Analysis ◽  
Restriction Enzymes ◽  
Rapid Identification ◽  
Starch Synthase ◽  
Amaranthus Caudatus ◽  
Grain Amaranth ◽  
Amaranthus Hypochondriacus ◽  
Pcr Rflp ◽  
Cultivated Species ◽  
Species Specific

The objective of this study was to develop a PCR–RFLP method to identity the cultivated species of grain amaranth based on variations in the sequences of their starch synthase genes. We sequenced the SSSI and GBSSI loci in 126 accessions of cultivated grain amaranth collected from diverse locations around the world. We aligned the gene sequences and searched for restriction enzyme cleavage sites specific to each species for use in the PCR–RFLP analysis. Our analyses indicated that EcoRI would recognize the sequence 5′-GAATT/C-3′ in the SSSI gene from Amaranthus caudatus L., and TaqI would recognize the sequence 5′-T/CGA-3′ in the GBSSI gene from Amaranthus hypochondriacus L. The PCR products obtained using gene-specific primers were 423 bp (SSSI) and 627 or 635 bp (GBSSI) in length. These products were cut with different restriction enzymes resulting in species-specific RFLP patterns that could be used to distinguish among the cultivated grain amaranths. The results clearly showed that A. caudatus and A. hypochondriacus were easily differentiated at the species level using this method. Therefore, the PCR–RFLP method targeting amaranth starch synthase genes is simple and rapid, and it will be a useful tool for the identification of cultivated species of grain amaranth.

scholarly journals Application of PCR – RFLP markers for identification of genetically delimited groups of the Calypogeia fissa complex (Jungermanniopsida, Calypogeiaceae)

2015 ◽  
Vol 38 (1) ◽  
pp. 1-8 ◽  
Author(s):  
Katarzyna Buczkowska
Keyword(s):  
North America ◽  
Scar Marker ◽  
Complex Structure ◽  
Restriction Enzymes ◽  
European Part ◽  
Rflp Markers ◽  
Genetic Studies ◽  
Pcr Product ◽  
Pcr Rflp ◽  
Restriction Sites

AbstractCurrently, two subspecies are formally recognized within Calypogeia fissa: C. fissa subsp. fissa occurring in Europe and C. fissa subsp. neogea known from North America. Genetic studies have revealed a complex structure of this species. Within the European part of distribution, three genetically distinct groups PS, PBand G are distinguished. The combination of the SCAR marker Cal04 and PCR-RFLP markers with three restriction enzymes (SmaI, TaqI and TspGWI) allowed the recognition of all groups within the C. fissa complex. The TaqI enzyme recognizing the restriction sites in the PCR product of SCAR marker Ca104 turned out to be the best marker

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