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.

scholarly journals Genetic diversity of <i>κ</i>-casein (<i>CSN3</i>) and lactoferrin (<i>LTF</i>) genes in the endangered Turkish donkey (<i>Equus asinus</i>) populations

2019 ◽  
Vol 62 (1) ◽  
pp. 77-82 ◽  
Author(s):  
Fulya Özdil ◽  
Hasan Bulut ◽  
Raziye Işık
Keyword(s):  
Restriction Enzyme ◽  
Animal Species ◽  
Restriction Enzymes ◽  
Production Traits ◽  
Single Nucleotide ◽  
Equus Asinus ◽  
Pcr Rflp ◽  
Hardy Weinberg Equilibrium ◽  
Polymerase Chain ◽  
Enzyme Recognition

Abstract. In this study, the κ-casein (CSN3) and lactoferrin (LTF) genes which were found in association with milk production traits in different animal species were studied firstly in Turkish donkey populations. A total of 108 donkeys from different regions of Turkey were used in order to reveal the different genotypes of CSN3 and LTF genes by using polymerase chain reaction – restriction fragment length polymorphism (PCR-RFLP) and DNA sequencing methods. To determine the genetic polymorphism, we attempted to digest a fragment of 235 bp of the CSN3 gene and a fragment of 751 bp of the LTF gene using PstI, and DraII, EagI and MboI restriction enzymes, respectively. Neither the CSN3 gene nor the LTF gene had enzyme recognition sites with the PstI, DraII and MboI restriction enzymes in all of the studied samples. However, the LTF gene was only distinguished with the EagI restriction enzyme. Three genotypes were identified in the LTF gene with the EagI restriction enzyme: GG homozygotes (667, 84 bp), AG heterozygotes (751; 667, 84 bp) and AA homozygotes (751 bp). The transition from guanine to adenine in 89 bp of the LTF gene lacks the restriction site and different genotypes are obtained. This novel single nucleotide polymorphism (SNP) has been firstly detected in donkeys. According to the results, the G allele was predominant in the LTF-EagI gene in the studied Turkish donkey populations. In this study, all the genotype distributions of LTF-EagI were not found in Hardy–Weinberg equilibrium (P<0.05). The CSN3 and LTF genes have not been studied before in donkeys, so the results are the preliminary results of these gene regions in donkeys.

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 Studying of cyp2c19*2, *3 and *17 polymorphism in Vietnamese patients with coronary artery disease

2020 ◽  
Vol 18 (1) ◽  
pp. 41-48
Author(s):  
Nguyen Hai Ha ◽  
Le Thi Bich Thao ◽  
Nguyen Thi Thanh Hoa ◽  
Le Thi Thu Hien
Keyword(s):  
Coronary Artery Disease ◽  
Coronary Artery ◽  
Restriction Enzymes ◽  
Metabolic Phenotype ◽  
Single Nucleotide ◽  
Pcr Rflp ◽  
Cyp2c19 Gene ◽  
Ultrarapid Metabolizers ◽  
Coronary Syndromes ◽  
Artery Disease

Coronary artery disease is the most common type of cardiovascular disease, due to the accumulation of atherosclerotic plaque inside the arterial wall which leads to block blood supply to the heart muscle. A number of clinical trials have demonstrated that Clopidogrel is able to inhibit platelet aggregation in patients with acute coronary syndromes, reduce mortality and cardiovascular events. However, the antiplatelet effectiveness of Clopidogrel significantly depends on CYP2C19 genotypes. Therefore, the aim of this study was to identify the CYP2C19*2, *3 and allele frequencies in Vietnamese coronary artery patients by using PCR-RFLP method. Total genomic DNA were extracted from peripheral blood of 96 patients diagnosed with coronary artery disease. Thereafter, single nucleotide polymorphism sites in the CYP2C19 gene were identified by PCR with specific primers. The amplified products were then digested by restriction enzymes SmaI, BamHI, and MnlI, respectively. The results showed that the proportion of heterozygous individuals for CYP2C19*2 (c. 681G>A, rs4244285), CYP2C19*3 (c. 636G>A, rs4986893), and CYP2C19*17 (g. -3402C>T, rs11188072) accounted for 39.58%, 6.25%, and 2.08%, respectively. Among 96 subjects, 41.67% of patients were predicted for intermediate metabolic phenotype CYP2C19*1/*2 (37.50%) and CYP2C19*1/*3 (4.17%). Approximately 10.42% of total patients represented poor metabolizers in which 8.34% had two copies of the same allele *2/*2 and 2.08% had *2/*3 genotype. Particularly, two individuals (2.08%) detected with CYP2C19*1/*17 genotype were able to increase CYP2C19 activity (ultrarapid metabolizers). The results of this study generate a foundation for introducing individualized antiplatelet therapy in Vietnam based on genetic testing.

scholarly journals Derived Polymorphic Amplified Cleaved Sequence (dPACS): A Novel PCR-RFLP Procedure for Detecting Known Single Nucleotide and Deletion–Insertion Polymorphisms

2019 ◽  
Vol 20 (13) ◽  
pp. 3193 ◽  
Author(s):  
Shiv Shankhar Kaundun ◽  
Elisabetta Marchegiani ◽  
Sarah-Jane Hutchings ◽  
Ken Baker
Keyword(s):  
Gel Electrophoresis ◽  
Restriction Site ◽  
Restriction Enzymes ◽  
Nucleotide Polymorphisms ◽  
Acetyl Coa Carboxylase ◽  
Wild Type ◽  
Single Nucleotide ◽  
Pcr Rflp ◽  
Broadleaf Species ◽  
Selection Of

Most methods developed for detecting known single nucleotide polymorphisms (SNP) and deletion–insertion polymorphisms (DIP) are dependent on sequence conservation around the SNP/DIP and are therefore not suitable for application to heterogeneous organisms. Here we describe a novel, versatile and simple PCR-RFLP procedure baptised ‘derived Polymorphic Amplified Cleaved Sequence’ (dPACS) for genotyping individual samples. The notable advantage of the method is that it employs a pair of primers that cover the entire fragment to be amplified except for one or few diagnostic bases around the SNP/DIP being investigated. As such, it provides greater opportunities to introduce mismatches in one or both of the 35–55 bp primers for creating a restriction site that unambiguously differentiates wild from mutant sequences following PCR-RFLP and horizontal MetaPhorTM gel electrophoresis. Selection of effective restriction enzymes and primers is aided by the newly developed dPACS 1.0 software. The highly transferable dPACS procedure is exemplified here with the positive detection (in up to 24 grass and broadleaf species tested) of wild type proline106 of 5-enolpyruvylshikimate-3-phosphate synthase and its serine, threonine and alanine variants that confer resistance to glyphosate, and serine264 and isoleucine2041 which are key target-site determinants for weed sensitivities to some photosystem II and acetyl-CoA carboxylase inhibiting herbicides, respectively.

scholarly journals KAJIAN VARIASI SEKUNES INTRASPESIES DAN FILOGENETIK MONYET HITAM SULAWESI (Macaca nigra) DENGAN MENGGUNAKAN GEN COI

2017 ◽  
Vol 17 (1) ◽  
pp. 59
Author(s):  
Fitri Elisabeth Br. Hasibuan ◽  
Feky R Mantiri ◽  
Rooije R.H Rumende
Keyword(s):  
Phylogenetic Analysis ◽  
Genetic Distance ◽  
Cytochrome Oxidase ◽  
Intraspecific Variation ◽  
Dna Sequences ◽  
Sequence Variation ◽  
Cytochrome Oxidase I ◽  
Coi Gene ◽  
Forest Conversion ◽  
Macaca Nigra

KAJIAN VARIASI SEKUNES INTRASPESIES DAN FILOGENETIK MONYET HITAM SULAWESI (Macaca nigra) DENGAN MENGGUNAKAN GEN COI ABSTRAKMacaca nigra merupakan salah satu spesies yang endemik dan terancam punah di Sulawesi Utara. Eksploitasi yang berlebihan serta alih fungsi hutan menjadi ancaman bagi spesies ini di alam. Penelitian ini dilakukan untuk mengetahui variasi sekuens intraspesies M. nigra yang berada di Pusat Penyelamatan Satwa Tasikoki Bitung. Analisis sekuens menunjukkan terdapat perbedaan sepuluh pasang basa nukleotida pada urutan sekuens sampel dilokasi yang berbeda. Jarak genetik antara kedua sampel yaitu 0.016. Hasil perhitungan jarak genetik menunjukkan variasi genetik masih berada dalam kisaran variasi intraspesies dengan ambang batas untuk variasi intraspesies yaitu 0.015-0.025. Selain itu, variasi juga ditunjukkan pada sampel dengan kerabat dekatnya yang terdata di GenBank disebabkan karena adanya mutasi sinonim dan mutasi nonsinonim. Analisis filogenetik berdasarkan gen COI (Cytochrome Oxidase-I) menunjukkan bahwa sampel M. nigra yang digunakan dalam penelitian ini berada satu klaster dengan M. nigra yang ada di database dan termasuk ke dalam kelompok Silenus.Kata kunci: Variasi sekuens intraspesies, Gen COI, Macaca nigra, analisis filogenetik. THE STUDY INTRASPECIFIC VARIATION SEQUENCES AND PHYLOGENETIC CELEBES BLACK MACAQUE (Macaca nigra) USING COI GENE ABSTRACTMacaca nigra is listed as one of the endemic species and endangered in North Sulawesi. Exploitation and forest conversion have become threats to this species in the wild. This study was conducted to determine the intraspecific sequence variation of M. nigra located in Tasikoki Wildlife Rescue Center, Bitung. Sequence analysis revealed ten nucleotides differences between these two specimens. Genetic distance for both of specimens is 0.016. The result of genetic distance, the genetic variation between the specimens of M. nigra was still within the range of intraspecific variation. Distance analysis was also conducted by comparing with the close relatives of M. nigra based on BLAST search, which showed range from 0.015-0.025. These differences resulted in both synonymous and nonsynonymous mutation. Phylogenetic analysis using DNA sequences of COI (Cytochrome Oxidase-I) gene revealed that the two specimens of M. nigra claster together with M. nigra sequences that have been deposited in GeneBank. Moreover M. nigra is claster in the silenus group which is in accordance with previous reports.Keywords: Intraspecific Sequence Variation, COI Gene, Macaca nigra, Phylogenetic analysis.

scholarly journals Genetic diversity in populations of Slovak Spotted cattle based on single nucleotide polymorphisms analyses.

1970 ◽  
Vol 60 (4) ◽  
Author(s):  
Nina Moravčíková ◽  
Anna Trakovická ◽  
Alica Navrátilová
Keyword(s):  
Genetic Diversity ◽  
Leptin Receptor ◽  
Genetic Relatedness ◽  
Polymorphic Information Content ◽  
Restriction Enzymes ◽  
Genetic Distances ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Pcr Rflp ◽  
Hardy Weinberg Equilibrium

The aim of this study was to identify SNPs in leptin (LEP), leptin receptor (LEPR) and growth hormone (GH) genes in order to analyze genetic diversity of Slovak Spotted cattle. The total numbers of blood samples were taken from 353 Slovak Spotted cows originating from four farms. Genomic DNA was isolated by phenol-chloroform extraction method and analyzed by PCR-RFLP method. After digestion with restriction, enzymes were detected in whole population of cow's alleles with frequency: LEP/Sau3AI A 0.84 and B 0.16 (±0.0152); LEPR/BseGI C 0.95 and T 0.05 (±0.0089) and GH/AluI L 0.70 and V 0.30 (±0.0188). Based on the observed vs. expected genotypes frequencies populations across loci were in Hardy-Weinberg equilibrium (P\>0.05). Predominant for SNP LEP/Sau3AI was AA genotype (0.70), for SNP LEPR/T945M CC genotype (0.91), and LL genotype (0.48) was most frequent for SNP GH/AluI. The observed heterozygosity of SNPs across populations was also transferred to the low or median polymorphic information content 0.24 (He 0.28), 0.08 (He 0.09) and 0.33 (He 0.47) for LEP, LEPR and GH genes, respectively. Within genetic variability estimating negative values of fixation indexes FIS (-0.09-0.05) and FIT (-0.07-0.03) indicating heterozygote excess were observed. The value of FST indexes (0.018-0.023) shows very low levels of genetic differentiation in allele frequencies of loci among evaluated subpopulations. The low values of genetic distances (0.0018-0.0159) indicated high genetic relatedness among animals in subpopulations caused probably by common ancestry used in breeding program at farms.

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