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

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 of PCR-RFLP Haplotypes For Assessing Genetic Variation in the Green Oak Leaf Roller Tortrix viridana L. (Lepidoptera, Tortricidae)

2005 ◽  
Vol 54 (1-6) ◽  
pp. 17-24 ◽  
Author(s):  
H. Schroeder ◽  
F. Scholz
Keyword(s):  
Cytochrome Oxidase ◽  
Intraspecific Variation ◽  
Restriction Enzymes ◽  
Cytochrome Oxidase I ◽  
Nucleotide Substitutions ◽  
Single Nucleotide ◽  
Genetic Studies ◽  
Leaf Roller ◽  
Pcr Rflp ◽  
Tortrix Viridana

Abstract PCR-RFLPs were performed to assess intraspecific variation in the green oak leaf roller, Tortrix viridana. The cytochrome oxidase I and II genes were amplified with universal and self designed primers, respectively, resulting in three PCR-fragments of 802 bp, 729 bp and 680 bp. 29 restrictions endonucleases were tested for variation in these PCR-patterns. Seven of these enzymes were chosen for further research. We found 13 haplotypes in four populations across a total of 436 individuals. In addition all haplotypes were sequenced. More single nucleotide substitutions were detected in the sequences, particularly in the middle of the cytochrome oxidase I gene, missed by the used restriction enzymes. For these markers intraspecific variation in T. viridana is high compared to other insect species. Furthermore we found differences in frequency of haplotypes among the investigated populations which induce that the markers developed so far are suitable for population genetic studies in T. viridana.

PCR-RFLP ANALYSIS OF THE CHLOROPLAST GENE trn K IN THE PINACEAE, WITH SPECIAL REFERENCE TO THE SYSTEMATIC POSITION OF CATHAYA

1998 ◽  
Vol 46 (4) ◽  
pp. 265-271 ◽  
Author(s):  
Xiao-Quan Wang ◽  
Ying Han ◽  
De-yuan Hong
Keyword(s):  
Molecular Phylogeny ◽  
Restriction Site ◽  
Rflp Analysis ◽  
Restriction Enzymes ◽  
Systematic Position ◽  
Chloroplast Gene ◽  
Parsimony Method ◽  
Pcr Rflp ◽  
Restriction Sites ◽  
Dollo Parsimony

The molecular phylogeny of the Pinaceae represented by 13 species of 10 genera was constructed from PCR-RFLP analysis of the chloroplast gene trn K, which was approximately 2557 bp long. Ninety-two restriction sites, of which 68 were variable, were identified by 16 restriction enzymes. Thirty-five of the 68 polymorphic sites were phylogenetically informative. The restriction site data were analyzed by PAUP (version 3.1.1) with both the Wagner parsimony method and the Dollo parsimony method. As a result, Dollo and Wagner parsimonious trees have similar topologies except for the position of Cedrus. The Abies-Keteleeria-Tsuga-Pseudolarix clade was well resolved in all trees. Pseudotsuga is closely related to Larix, while Abies is relatively closely related to Keteleeria. As an isolated genus, Cathaya is distantly related to the Abies-Keteleeria-Tsuga-Pseudolarix clade, and is not very closely related to any other genus of the Pinaceae.

scholarly journals Genetic Variation in Cytochrome b-Hinf1 and -Alu1 Gene Correlated to Body Size in Soang Gourami (Osphronemus goramy Lacepede, 1801) from Single Spawning

2017 ◽  
Vol 9 (2) ◽  
Author(s):  
Agus Nuryanto ◽  
Nael Huda Qonita ◽  
Hendro Pramono ◽  
Kusbiyanto Kusbiyanto ◽  
Petrus Hary Tjahja Soedibja
Keyword(s):  
Genetic Variation ◽  
Body Size ◽  
Cytochrome B ◽  
Restriction Enzymes ◽  
Cytochrome B Gene ◽  
Rflp Marker ◽  
Rflp Markers ◽  
Molecular Technique ◽  
Pcr Rflp ◽  
Body Sizes

<p>Soang gourami fingerling shows variable body sizes eventhough resulted from single spawning. Differences in body sizes among individuals is assumed to be correlated to their genetic component which can be studied using cytochrome b gene PCR-RFLP marker. This study aimed to determine specific PCR-RFLP marker among different sizes of soang gourami collected from single spawning. Genomic DNA was isolated using Chelex method. Cytochrome b gene were amplified and digested using four restriction enzymes. Specific markers were analyzed descriptivelly based on DNA band pattern appear in agarose gel. Ther result showed that PCR-RFLP markers of Cytochrome b-<em>Hinf</em>I of 315bp, and 210bp, and also Cytochrome b-<em>Alu</em>I of 334bp and 189bp are specific markers for large individuals, whereas small individuals are characterized by having Cytochrome b-<em> Hinf</em>I 366bp, and 159bp and Cytochrome b-<em>Alu</em>I 525bp fragments. It is observed that genetic variation of Cytochrome b-<em>Hinf</em>I and -<em>Alu</em>I markers are possitively correlated to body size in soang gourami fingerling. Therefore, both cytochrome b-<em>Hinf</em>I and -<em>Alu</em>I gene can be reffered as specific markers to differentiate among different sizes of soang gourami strain fingerling from single spawning. This result proved that genetic divergences among individuals can be related with certain quantitative characters, such size related. Therefore our study can contribute on fisheries development, especially by providing new technique for fingerling selection to obtain high quality fingerling and also provide new insight the application of molecular technique in fisheries. </p>

Rapid and reliable identification of rice genomes by RFLP analysis of PCR-amplified Adh genes

Genome ◽  
2001 ◽  
Vol 44 (6) ◽  
pp. 1136-1142 ◽  
Author(s):  
Song Ge ◽  
Tao Sang ◽  
Bao-rong Lu ◽  
De-yuan Hong
Keyword(s):  
Rflp Analysis ◽  
Restriction Enzymes ◽  
Pcr Primers ◽  
Specific Pcr ◽  
Adh Genes ◽  
Pcr Rflp ◽  
Restriction Sites ◽  
Pcr Products ◽  
Adh Gene ◽  
Genus Oryza

The rice genus (Oryza L.) consists of 24 species with 10 recognized genome types. With the realization of many useful genes in species of wild rice, continuous efforts have been made to understand their genomic composition and relationships. However, the identification of rice genomes has often been difficult owing to complex morphological variation and formation of allotetraploids. Here we propose a rapid and reliable method for identifying rice genomes based on the restriction sites of PCR-amplified Adh genes. The experimental procedure was as follows: (i) amplify a portion of Adh1 and Adh2 genes with the locus-specific PCR primers; (ii) digest PCR products with restriction enzymes that distinguish different genomes; and (iii) run the digested products on 1.4% agarose gel, and photograph. Using various combinations of restriction digestion of the two Adh genes, all of the rice genomes can be identified.Key words: Adh gene, genome, identification, Oryza L., PCR–RFLP.

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 Genetic Homogenity of Commerson’s Anchovy (Stolephorus commersonnii) in Segara Anakan Cilacap Central Java Inferred from PCR-RFLP Markers

2019 ◽  
Vol 7 (1) ◽  
pp. 14
Author(s):  
Agus Nuryanto ◽  
Rani Eva Dewi ◽  
Hendro Pramono
Keyword(s):  
Genetic Diversity ◽  
Restriction Enzymes ◽  
Coi Gene ◽  
Survey Method ◽  
Rflp Markers ◽  
Small Pelagic Fish ◽  
Central Java ◽  
Low Genetic Diversity ◽  
Pcr Rflp ◽  
Pcr Products

Commerson’s anchovy (Stolephorus commersonnii) is a small pelagic fish that live in a group and its existence is very abundant in Segara Anakan Cilacap. This anchovy is widely consumed by communities live around Segara Anakan. This leads to a high exploitation rate. Exploited populations generally have low genetic diversity. This study aims to evaluate genetic diversity of commerson’s anchovy population in Segara Anakan Cilacap inferred from PCR-RFLP of the cytochrome c oxidase 1 (CO1) gene. This study was conducted from January to April 2018 and used survey method by applying random sampling. As many as 30 samples of anchovy were taken. Genomic mtDNA was isolated using modified Chelex method. Partial sequences of the COI gene were amplified using a pair forward commercially available primer. The lengths of 650 base pair of the PCR products were digested with four restriction enzymes. The HindIII enzyme produces PCR-RFLP fragment with the size of 416 bp and 234 bp lengths, VspI produces 435 bp and 214 bp, CO1-TaqI produces 556 bp and 94 bp and RsaI produces 319 bp, 183 bp, and 148 bp fragments, respectively. The PCR-RFLP fragments were obtained from all samples but they produced uniform band pattern for all 30 anchovy individuals. These results indicated that the anchovy population in Segara Anakan Cilacap has monomorphic allele for all PCR-RFLP markers. Hence, it can be concluded that genetic homogenity was observed on anchovy population in Segara Anakan Cilacap as inferred from PCR-RFLP COI gene.

scholarly journals Frequencies of CYP2B6∗4,∗5, and ∗6 Alleles within an Iranian Population (Mazandaran)

2021 ◽  
Vol 2021 ◽  
pp. 1-6
Author(s):  
Mohammad Bagher Hashemi-Soteh ◽  
Elaheh Hosseini ◽  
Shokoufeh Fazelnia ◽  
Faramarz Ghasemian-Sorbeni ◽  
Sara Madahian ◽  
...  
Keyword(s):  
Ethnic Group ◽  
Ethnic Diversity ◽  
Gel Electrophoresis ◽  
Restriction Enzymes ◽  
Iranian Population ◽  
Agarose Gel ◽  
Agarose Gel Electrophoresis ◽  
Cytochrome P450 2B6 ◽  
Pcr Product ◽  
Pcr Rflp

Background. The human CYP2B subfamily consists of one functional gene (CYP2B6) and one pseudogene (CYP2B7P). Cytochrome P450 2B6 (CYP2B6) is a highly polymorphic enzyme that shows marked interindividual and interethnic variations. Currently, 38 alleles have been described, and some of the allelic variants have been associated with low enzyme activity. The aim of this study was to investigate the frequencies of CYP2B6∗4, CYP2B6∗5, and CYP2B6∗6 alleles in the Mazani ethnic group among Iranian Population. Methods. The study was conducted in 289 unrelated healthy volunteers. DNA was extracted from peripheral blood and analyzed by the PCR-RFLP protocol. The PCR product was digested with restriction enzymes and then separated using agarose gel electrophoresis. Results. The frequency of CYP2B6∗4, CYP2B6∗5, and CYP2B6∗6 in this study was 34.60%, 7.26%, and 34.54%, respectively. Conclusion. The frequency of the CYP2B6∗4 allele in the Mazani ethnic group was much higher (34.60%) than other population. The frequency of CYP2B6∗6 (34.54%) also was higher than its frequency in other previously reported population. But the frequency of CYP2B6∗5 in this study was lower than expected. These results will be useful in understanding the ethnic diversity in Iranian population and offer a preliminary basis for more rational use of drugs that are substrates for CYP2B6 in this population.

scholarly journals Molecular variation in chloroplast DNA regions in ancestral species of wheat.

Genetics ◽  
1994 ◽  
Vol 137 (3) ◽  
pp. 883-889 ◽  
Author(s):  
N T Miyashita ◽  
N Mori ◽  
K Tsunewaki
Keyword(s):  
Chloroplast Dna ◽  
Restriction Enzymes ◽  
Triticum Dicoccoides ◽  
The Other ◽  
Major Type ◽  
Aegilops Speltoides ◽  
Triticum Timopheevi ◽  
Restriction Sites ◽  
D Values ◽  
Chloroplast Dna Regions

Abstract Restriction map variation in two 5-6-kb chloroplast DNA regions of five diploid Aegilops species in the section Sitopsis and two wild tetraploid wheats, Triticum dicoccoides and Triticum araraticum, was investigated with a battery of four-cutter restriction enzymes. A single accession each of Triticum durum, Triticum timopheevi and Triticum aestivum was included as a reference. More than 250 restriction sites were scored, of which only seven sites were found polymorphic in Aegilops speltoides. No restriction site polymorphisms were detected in all of the other diploid and tetraploid species. In addition, six insertion/deletion polymorphisms were detected, but they were mostly unique or species-specific. Estimated nucleotide diversity was 0.0006 for A. speltoides, and 0.0000 for all the other investigated species. In A. speltoides, none of Tajima's D values was significant, indicating no clear deviation from the neutrality of molecular polymorphisms. Significant non-random association was detected for three combinations out of 10 possible pairs between polymorphic restriction sites in A. speltoides. Phylogenetic relationship among all the plastotypes (plastid genotype) suggested the diphyletic origin of T. dicoccoides and T. araraticum. A plastotype of one A. speltoides accession was identical to the major type of T. araraticum (T. timopheevi inclusively). Three of the plastotypes found in the Sitopsis species are very similar, but not identical, to that of T. dicoccoides, T. durum and T. aestivum.

scholarly journals Development of the Multiple Gene Knockout System with One-Step PCR in Thermoacidophilic Crenarchaeon Sulfolobus acidocaldarius

Archaea ◽  
2017 ◽  
Vol 2017 ◽  
pp. 1-12 ◽  
Author(s):  
Shoji Suzuki ◽  
Norio Kurosawa
Keyword(s):  
Gene Knockout ◽  
Arginine Decarboxylase ◽  
Sulfolobus Acidocaldarius ◽  
Dna Photolyase ◽  
Genetic Studies ◽  
Multiple Gene ◽  
Plasmid Construction ◽  
Pcr Product ◽  
Optimized Protocol ◽  
One Step

Multiple gene knockout systems developed in the thermoacidophilic crenarchaeon Sulfolobus acidocaldarius are powerful genetic tools. However, plasmid construction typically requires several steps. Alternatively, PCR tailing for high-throughput gene disruption was also developed in S. acidocaldarius, but repeated gene knockout based on PCR tailing has been limited due to lack of a genetic marker system. In this study, we demonstrated efficient homologous recombination frequency (2.8 × 104 ± 6.9 × 103 colonies/μg DNA) by optimizing the transformation conditions. This optimized protocol allowed to develop reliable gene knockout via double crossover using short homologous arms and to establish the multiple gene knockout system with one-step PCR (MONSTER). In the MONSTER, a multiple gene knockout cassette was simply and rapidly constructed by one-step PCR without plasmid construction, and the PCR product can be immediately used for target gene deletion. As an example of the applications of this strategy, we successfully made a DNA photolyase- (phr-) and arginine decarboxylase- (argD-) deficient strain of S. acidocaldarius. In addition, an agmatine selection system consisting of an agmatine-auxotrophic strain and argD marker was also established. The MONSTER provides an alternative strategy that enables the very simple construction of multiple gene knockout cassettes for genetic studies in S. acidocaldarius.

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