Microsatellite dna pdf thesis

Population structure of spotted seatrout, cynoscion nebulosus, in texas bays and estuaries as revealed by analysis of microsatellite dna. Request pdf evolutionary dynamics of microsatellite dna within the past decade microsatellites have developed into one of the most popular genetic markers. Dna was extracted from the coral samples using qiagen dna extraction kit. Microsatellite dna mutations and polycyclic aromatic hydrocarbon pah metabolites in wild doublecrested cormorants phalacrocorax auritus from hamilton harbour associated with exposure to airborne pollutants by laura king, b. Microsatellite dna marker analysis of genetic variation in. Despite the wide applicability of ssrs as genetic markers since their discovery in the 1980s, little is known about the biological importance of microsatellites tautz and renz, 1984, especially in plants. In this thesis, i focus on studying human evolution through the use of microsatellites, which are simple repetitive sections of dna of typically 16bp motifs e. Since several authors suggested that loggerhead shrike completed their preformative and formative molt on the breeding grounds prior to fall migrations, i. The dna was then screened using pcr and 8 microsatellite markers. Population genetic structure of new zealand blue cod. For the last 30 years, attempts have been made to discriminate among fish populations by using molecular markers. Isolation and characterization of microsatellite dna. One way to assess the genetic diversity is through the use of microsatellite molecular markers. The application of microsatellite dna markers for forensic analysis of koi carp cyprinus carpioj.

British columbian killer whales based on 11 microsatellite loci, using neis standard genetic distances. Speciesspecific microsatellite primers mcga5, mcga7, mcga10, mcga12, mcca9. One of the most common genetic changes in bladder cancer is loss of heterogeneity in chromosome 9 50. These loci have the power to provide the most comprehensive. Despite the widespread use of microsatellite analysis, an integral picture of the mutational dynamics of microsatellite dna is just beginning to emerge. Parapercis colias blue cod is an endemic temperate reef fish that supports an important commercial and recreational fishery in new zealand. Amplification of the genomic dna was carried out using a panel of twenty eight microsatellite sites specific primer pairs covering all the chromosomes existing in the genome. Tandemly repeated dna may see in theliterature as strs short tandem repeats poly at most common 110 bp tandemly repeated micro satellite 10 mini satellitetypes of microsats di, tetra and tri nucleotide used in that order perfect imperfectinterrupted compound. A microsatellite enriched library was constructed with dna obtained from the lychee cultivar hong huay, which is maintained at the experimental farm of kinki university, japan. The hsv2 isolates were selected retrospectively from viral isolates obtained in cell culture and stored in the laboratory between 2005 and 2012, in order to obtain a range of viruses collected from both immunocompetent and immunosuppressed mainly hiv. A thesis submitted to the school of graduate studies in partial fulfilment of the. Shaw pw, pierce gj, boyle pr 1999 subtle population structuring within a highly vagile marine invertebrate, the veined squid loligo forbesi, demonstrated with microsatellite dna markers. A key challenge is to understand and characterize the evolution of the variability between human genomes. Thesis on killer whales department of zoology at ubc.

Caratterizzazione di marcatori microsatellitari in pancratium maritimum l. A total of 105,015 reads with an average read length of 393 bp containing 1,234 possible microsatellite sites were obtained. Microsatellite variability of two populations of clarias. Cells with a dysfunctional mmr protein accumulate errors when the loop resulting in frameshift mutations indels, leading to the appearance of novel alleles at microsatellite loci, which can be easily identified via fragment analysis. Microsatellite analysis msa is a pcr analysis of dna in exfoliated urine cells.

Pdf markers for eight new microsatellite dna or simple sequence repeat ssr loci were developed and characterized in trembling aspen populus. To amplify microsatellite loci by polymerase chain reaction pcr, primers must be developed from the dna that flanks specific microsatellite repeats. Tendency of an organism to stay in or return to habitat. District head quarter dhq hospital, faisalabad, pakistan. They have a higher mutation rate than other areas of dna leading to high genetic diversity. A practical approach to microsatellite genotyping with. Carlos lopez, along with sylvie augustin, supervised roman and neus msc thesis. Herpes simplex virus 2 hsv2, classified together with hsv1 in the alphaherpesvirinae subfamily, is a highly prevalent sexually transmitted infection worldwide. Secondo vari studi filogenetici basati sulle sequenze del dna plastidiale. Minisatellite dna, sometimes called variable number tandem repeats vntrs, is composed of blocks of longer repeats also dispersed throughout the genome. They have also become the primary marker for dna testing in forensics court contexts both for human and wildlife cases e. Evidence of female philopatry and malebiased gene flow among regional populations of the blue andyellow macaw psittaciformes. Informativeness of these microsatellite dna markers was examined by determining polymorphisms in 38 p.

Markers for eight new microsatellite dna or simple sequence repeat ssr loci were developed and characterized in trembling aspen populus tremuloides from a partial genomic library. I certify that this thesis satisfies all the requirements as a thesis for the. Microsatellite dna markers in populus tremuloides spectrum. Best online thesis writing services, professional thesis writing services, and master thesis writing services at low cost. Genetic diversity of european black poplar populus.

Microsatellites or single sequence repeats ssrs are extensively employed in plant genetics studies, using. Tandemly repeated dna may see in theliterature as strs short tandem repeats poly at most common 110 bp tandemly repeated micro satellite 10 mini satellitetypes of microsats di, tetra and tri nucleotide used in that order perfect. Microsatellite dna variants of four ssr loci characterized previously followed a singlelocus mendelian inheritance pattern, whereas those of ptr7 from the present study showed a twolocus mendelian inheritance pattern in controlled crosses. Isolation and characterization of microsatellite dna markers. Developing microsatellite primers for cave amphipod. Mitochondrial and microsatellite dna markers reveal a. Within the past decade microsatellites have developed into one of the most popular genetic markers.

Microsatellite markers are codominant, polymorphic dna loci containing repeated nucleotide sequences, typically with 2 to 10 nucleotides per repeated unit. Recently many investigators have used microsatellite dna loci for studying the evolutionary relation ships of closely related populations or species, and some authors proposed new genetic distance measures for this purpose. Population structure of spotted seatrout, cynoscion. Microsatellitebased phylogenetic tree analysis of australian. However, the efficiencies of these distance measures in obtaining the correct tree topology remains unclear.

Mehlenbacher european hazelnut is a significant crop in the pacific northwest, and the us ranks. These findings also suggested that species and taxonomic origin of microsatellite loci were both significant predictors of microsatellite heterozygosity in rhinoceroses. The use of neutral molecular markers, such as microsatellite dna length polymorphisms, can provide more direct estimates of the extent of population genetic structure between populations, and as such can be utilized to assess the extent to which hadal trenches represent demographically and evolutionarily independent units. Microsatellite marker analysis thermo fisher scientific in. Dna from each oyster was amplified using pcr for each microsatellite marker. An abstract of the thesis of oregon state university. Cacacacaca that are highly polymorphic and highly mutable. Hence, the possibility of generating a concise database for microsatellite markers of a variety of prunus varieties is to be assessed in the second chapter of this thesis. Using microsatellite dna to genetically identify a. Abstract genetic markers are useful in identification of various genetic variations.

This study assessed whether carp nurseries could be distinguished based on differences in 12 microsatellite dna markers in carp across the twin cities metropolitan area n1023 and the concentrations of 11 trace elements measured in carp otoliths collected in the sixmile creek subwatershed, minnesota, usa n157. Importance, uses and applications shahid raza 1, muhammad waseem shoaib2 and hira mubeen 1. We offer a full service which includes assistance in designing and ordering fluorescently labeled primer pairs for the microsatellite markers of your choice. Each consists of a short base sequence, generally 210 bp long, that is repeated a variable number of times in a tandem array at any given locus.

Emmanuelle magnoux is research assistant in the molecular lab at inra orleans. Molecular characterization of herpes simplex virus 2 strains. Cd genomics has extensive experience in providing support for the selection and design of microsatellite markers for a wide range of plant and animal species. Dna markers and characterization of novel sources of eastern filbert blight resistance in european hazelnut corylus avellana l. Microsatellite dna markers for the study of population structure in the new.

Microsatellite dna an overview sciencedirect topics. Dna that was extracted and purified from populations of montastraea cavernosa and porites astreoides were used in the development of microsatellite primers. Rodolphe rougerie is a systematist working on dna barcoding of lepidoptera. Spiraea virginiana using microsatellite markers by honors. Pdf microsatellites or single sequence repeats ssrs are extensively employed in plant genetics studies, using both low and high. Hallermanc we describe the use of microsatel lite dna markers, previously developed for common carp, to investigate. Microsatellites based allelic diversity data were utilized for classification and formation of heterotic groups of the inbred lines. Of 153 microsatellite loci detected in the dna sequences, 94 primer pairs were tested for amplification and polymorphism in a panel of 12 vaccinium germplasm accessions. This study focused on developing new microsatellite markers from hazelnut transcriptome sequences and on disease resistance from three accessions culpla, crvenje, and osu 495. Graduate thesis or dissertation microsatellite marker. Microsatellite dna loci have become important sources of genetic information for a variety of purposes goldstein and schlotterer, 1999 see chapter 14. Molecular ecology, 8, 407417 tautz d 1989 hypervariability of simple sequences as a general source for polymorphic dna markers. Evaluating the ability of microsatellite dna markers and. However, concerns have been raised about localized stock depletion, and multiple lines of evidence have suggested p.

In recent years, south african forensic services have been expanded to include game species and marine fish stock identification. Chromosomes 4p, 8p, 9p, 11p, and 17p also often display loss of heterogeneity in patients with bladder cancer. Genetic diversity of european black poplar populus nigra. Presented in partial fulfillment of the requirements for graduation. The two perfect dinucleotide and one trinucleotide microsatellite dna loci were the most informative. Molecular characterization of herpes simplex virus 2. A microsatelliteenriched library was constructed with dna obtained from the lychee cultivar hong huay, which is maintained at the experimental farm of kinki university, japan. The set of observable characteristics of an individual resulting from the interaction of its genotype with the environment. They do so by recognizing a temporary insertiondeletion loop that is created when dna polymerase slips.

Using microsatellite dna to genetically identify a potential. A microsatellite is a tract of repetitive dna in which certain dna motifs ranging in length from one to six or more base pairs are repeated, typically 550 times. D measurements from feathers provide information on latitude of origin, while dna can be related to an affiliation to a breeding population. The ability of a population to adapt to a changing environment depends on its genetic variation. The dna of the twenty 20 specimens from each population extracted from the muscle tissue using phenolchloroform extraction pce method was subjected to microsatellite dna analysis. The number of nucleotides in the repeated unit is the same for the majority of the repeats within an individual microsatellite locus, but the number of repeats for a specific locus may. Thus, the study of genetic diversity within and among species or populations is especially important on conservation biology scopes. Although some techniques have proved successful in certain circumstances, the consistent trend to newer markers among fishery geneticists highlights the general lack of resolving power observed with older technologies. Merav bendavid, who is an inspiration to us all and provided me with many wonderful opportunities. Dna was extracted using a standard ctab procedure doyle and doyle, 1987. Molecular markers a tool for exploring genetic diversity.

To amplify microsatellite loci by polymerase chain reaction pcr, primers must be developed from the dna that flanks specific. The resulting dna was quantified using a nanodrop v3. Microsatellite dna markers for the study of population. Genetic distances and reconstruction of phylogenetic trees. That is, certain microsatellite alleles are associated through genetic linkage with certain mutations in coding regions of the dna that can cause a variety of medical disorders. Honors thesis development of microsatellite primers for. A genomic library was constructed from dna extracted from the blood of a female guinea fowl, using the nextgeneration sequencer. A total of 56 hsv2 clinical isolates and 2 laboratory strains ghsv2 and ms were included in the present study. Repetitive dna in certain dna motifs, ranging in length from 2 to 5 base pairs. Microsatellites occur at thousands of locations within an organisms genome. Hence, for example, one individual might have 17 consecutive repeats of the sequence. Seven 7 microsatellite markers cga01, cga02, cga03, cga05, cga06, cga09 and cga10 were used in the analysis. Using microsatellite dna to genetically identify a potential hybrid population of endangered massasauga rattlesnakes sistrurus catenatus in north central missouri.