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Carter, Deidre Anne. "DNA polymorphisms as genetic markers in Phytophthora infestans." Thesis, Imperial College London, 1991. http://hdl.handle.net/10044/1/46699.
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Laughlin, Thomas Fain. "Hypervariable DNA markers and population structure in three fish species." Diss., This resource online, 1993. http://scholar.lib.vt.edu/theses/available/etd-06062008-171854/.
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Valdman, Alexander. "Molecular genetic markers of prostate cancer development /." Stockholm, 2003. http://diss.kib.ki.se/2003/91-7349-618-9/.
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Silva, E. P. da. "Population genetic studies of the mussel Mytilus using nuclear DNA markers." Thesis, Swansea University, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.639035.
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The genetics of the mussel Mytilus is one of the most extensively studied among the marine invertebrates. This work is concerned with the use of nuclear DNA polymorphisms to study aspects of Mytilus population genetics. Sixteen populations of three species, M. edulis, M. galloprovincialis and M. trossulus were studied for 6 nDNA markers. SSCP analysis was used to enhance the variability in the N118 anonymous scnDNA region, a PCR fragment which previously showed little RFLP variation, and in a second PCR product from a nrDNA internal transcribed spacer region. In the first case, the number of alleles increased from 4 to 7 and the FST estimate from 0.0072 to 0.0096. In the second case, four alleles were resolved and a statistically significant FST value of 0.08 was revealed. Also, primers for an intron of myosin heavy chain was developed and fifteen alleles were resolved. Three of the alleles are M. trossulus specific, but the others show significant frequency differences among different species and even among populations in the same species. Analysis of the nuclear DNA population structure in M. edulis showed statistical significant levels of geographic variation, and when compared with allozymes revealed significant differences between the two sets of markers. This result is consistent with the operation of balancing selection on allozymes. Moreover, the use of the Ewens-Watterson homozygosity test revealed for the nDNA polymorphism a departure from a strictly neutral model, indicating that assumptions about the neutrality of a DNA polymorphisms could also be under suspicion. Evolutionary relationships between the three mussel species using nDNA markers are in line with morphological and allozymes studies, which show M. edulis as more closely related to M. galloprovincialis than to M. trossulus. However, a much higher level of differentiation than previously reported was found between the three taxa.
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Syaifudin, Mochamad. "Species-specific DNA markers for improving the genetic management of tilapia." Thesis, University of Stirling, 2015. http://hdl.handle.net/1893/22624.
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The tilapias are a group of African and Middle Eastern cichlid fish that are widely cultured in developed and developing countries. With many different species and sub-species, and extensive use of interspecies hybrids, identification of tilapia species is of importance in aquaculture and in wild populations where introductions occur. This research set out to distinguish between tilapia species and sub-species by retrieving species-specific nuclear DNA markers (SNPs) using two approaches: (i) sequencing of the coding regions of the ADA gene; and (ii) next-generation sequencing, both standard RADseq and double-digest RADseq (ddRADseq). The mitochondrial DNA (mtDNA) marker cytochrome c oxidase subunit I (COI) was used to verify tilapia species status. ADA gene sequence analysis was partially successful, generating SNP markers that distinguished some species pairs. Most species could also be discriminated using the COI sequence. Reference based analysis (RBA: using only markers found in the O. niloticus genome sequence) of standard RADseq data identified 1,613 SNPs in 1,002 shared RAD loci among seven species. De novo based analysis (DBA: based on the entire data set) identified 1,358 SNPs in 825 loci and RBA detected 938 SNPs in 571 shared RAD loci from ddRADseq among 10 species. Phylogenetic trees based on shared SNP markers indicated similar patterns to most prior phylogenies based on other characteristics. The standard RADseq detected 677 species-specific SNP markers from the entire data set (seven species), while the ddRADseq retrieved 38 (among ten species). Furthermore, 37 such SNP markers were identified from ddRADseq data from a subset of four economically important species which are often involved in hybridization in aquaculture, and larger numbers of SNP markers distinguished between species pairs in this group. In summary, these SNPs are a valuable resource in further investigating hybridization and introgression in a range of captive and wild stocks of tilapias.
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Bishop, Alexander James Roy. "The dynamics of minisatellite changes during meiosis in the yeast Saccharomyces cerevisiae." Thesis, University of Oxford, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.339351.
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Prodöhl, Paulo A. "Multilocus and single locus minisatellite DNA polymorphism in brown trout (Salmo trutta L.) populations." Thesis, Queen's University Belfast, 1993. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.296801.
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Bentley, Elizabeth. "Genetic analysis of the myelencephalic blebs mutation on mouse chromosome." Thesis, University College London (University of London), 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.265754.
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Honing, Jennifer. "Evaluation and implementation of DNA-based diagnostic methodology to distinguish wheat genotypes." Thesis, Link to the online version, 2007. http://hdl.handle.net/10019/638.
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Kremer, Kristin. "Genetic markers for Mycobacterium tuberculosis characterization and spread of the Beijing genotype /." [S.l. : Amsterdam : s.n.] ; Universiteit van Amsterdam [Host], 2005. http://dare.uva.nl/document/78818.
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Wu, Lizhao. "Molecular population genetic analyses of Lake Victoria Cichlid Fishes using microsatellite DNA markers /." The Ohio State University, 1999. http://rave.ohiolink.edu/etdc/view?acc_num=osu1488190595940009.
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Kamara, Davida F. "Development and characterization of DNA markers for two avian species." Thesis, Virginia Tech, 2006. http://hdl.handle.net/10919/42868.
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Central to the application of genomics to animal agriculture are DNA markers, especially microsatellites and single nucleotide polymorphisms. These markers are the resources necessary for constructing genetic maps and for determining how improved and unimproved animal breeds are related. Here, DNA markers were developed for two avian species, the turkey, Meleagris gallopavo, and the budgerigar (budgie), Melopsittacus undulatus. Genomic libraries enriched for simple sequence repeats were used to generate about 70 budgie sequences of a total length of 38 kb. From these sequences, 9 primer pairs were designed and used to screen for informativeness in a panel of DNA samples from unrelated budgie samples. All but one of the nine primers evaluated were polymorphic with the number of alleles ranging from two to four. Comparative analysis involving the use of these budgie primers showed moderate sequence similarity to turkey and chicken. The genomic libraries and the comparative sequences provide useful genomic reagents that could be used to construct a budgie genome map. In the turkey, ten previously described microsatellites and a gene-based single nucleotide polymorphism (SNP) were used to evaluate the relatedness of heritage varieties to a commercial strain. Estimates of Nei's genetic distance (D) and genetic differentiation (Rst) between populations using microsatellite markers showed that the commercial strain is genetically more closely related to the Bourbon Red and Narragansett and least related to the Royal palm and Spanish Black. Gene flow (Nm) level was highest between the commercial and Bourbon Red populations. The SNP analysis by PCR-RFLP revealed that the commercial strain was more closely related to the Spanish black and Narragansett and least related to the Bourbon red and Blue slate. Though results of the two marker systems, microsatellite and SNP, were inconsistent, they provide insights into using heritage turkeys to genetically improve commercial populations by introgression. The present thesis investigation showed that DNA markers provide a strong opportunity to develop genomic reagents needed to test hypotheses in little-studied agriculturally important and model avian species.Master of Science
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Rendell, Sarah. "Population genetic structure of Faidherbia albida (Del.) A. Chev. (Leguminosae, Mimosoideae)." Thesis, University of Oxford, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.299160.
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Safina, Melania. "DNA barcoding of Pleuronectiformes: in silico analysis and development of markers." Master's thesis, Alma Mater Studiorum - Università di Bologna, 2016. http://amslaurea.unibo.it/12259/.
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DNA barcoding is a method used for the identification and discovery of animal species. It usually involved a 648 base pair fragment of the mitochondrial cytochrome c oxidase subunit I, known as COI. This work is focused on the study of the genetic identification in the families belonging to the order Pleuronectiformes, commonly known as flatfish, and the accuracy of the genetic marker most used for the study of their DNA barcodes. The results indicate possible existence of taxonomical mistakes because several families do not show a gap between maximum intraspecific distance - which is the maximum distance within a specie - and the minimum interspecific distance - which is the minimum distance between a species and its nearest neighbor (NN), meaning that the marker in use cannot reliably distinguish among those species. This study uses a bioinformatic approach to design new Pleuronectiformes barcodes and compares their coverage and resolving power with that of existing barcodes. The new primers, proposed by the program EcoPrimer, are based on two indices that estimate the resolution capacity of the barcodes and the taxonomic coverage of them, for the amplification. The performances of both barcoding regions already in use (COI and 16 rDNA genes), and the new primer pairs designed, were performed through a ‘in silico PCR’. The results show that the new primer pairs, located in a different regions of 16S rDNA gene compared to the universal barcode region used in fishes, present best resolution capacity and taxonomic coverage than the others already in use. This is an essential complement for future barcoding studies.
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Allnutt, Theodore Richard. "The study of genetic variation in trees using the random amplified polymorphic DNA (RAPD) technique." Thesis, Liverpool John Moores University, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.319848.
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Laird, Alexander. "Molecular prognostic markers in renal cell carcinoma." Thesis, University of Edinburgh, 2015. http://hdl.handle.net/1842/17873.
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Renal cell carcinoma (RCC) is the most deadly of urological malignancies. While metastatic disease affects one third of patients at diagnosis, a further third of patients who undergo extirpative surgery with curative intent subsequently develop metastatic disease. Inconsistency in the clinical course ensures predicting subsequent metastasis is notoriously difficult, despite the routine use of prognostic clinico-pathological parameters in risk stratification. With greater understanding of pathways involved in disease pathogenesis, a number of biomarkers have been proposed to be of prognostic significance; however there are currently no molecular prognostic markers in clinical use. Genetic intra-tumoural heterogeneity (genetic ITH) has been described in clear cell RCC (ccRCC) and may limit the clinical translation of biomarkers. There has been no assessment of ITH at other molecular levels. The aim of this work was to define and compare proteomic, transcriptomic and DNA methylation ITH in ccRCC, and identify potential prognostic biomarkers. Using reverse phase protein arrays to study protein expression in multiple spatially separate regions of primary and metastatic ccRCC, proteomic ITH was demonstrated for the first time. Interestingly there was no significant difference in proteomic ITH in metastatic ccRCC tumour deposits compared to primary tumours. However, on analysis of differential protein expression between primary and metastatic ccRCC tissue using a tissue microarray and automated analysis of immunofluorescence, there was significantly greater expression of Ki67, p53, VEGFR1, SLUG and SNAIL in the metastases compared to the primary tumours. Subsequent profiling of gene expression and DNA methylation in multiple areas of the same primary tumours confirmed transcriptomic and methylomic ITH. On comparison of this multimolecular ITH, significantly greater proteomic ITH was seen compared to gene expression and DNA promoter methylation heterogeneity. Recent evidence suggests DNA methylation may be prognostically important in RCC and given the lower methylomic ITH in ccRCC, the identification of prognostic DNA methylation changes in ccRCC were pursued using the Infinium HumanMethylation450K Beadchip. Following development of an analysis pipeline, identification and validation of prognostic differentially methylated regions (DMR) was performed on an experimental cohort and published dataset respectively. Five DMRs, which were associated with disease recurrence in ccRCC, were identified. NEFM gene promoter methylation was the only DMR associated with cancer specific survival, independent of TNM stage and nuclear grade on multivariate analysis, which was confirmed on a third independent published dataset. This thesis therefore demonstrates multi-molecular ITH in ccRCC for the first time. Despite this, NEFM promoter methylation may be a useful independent prognostic marker of cancer specific survival.
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Jean, Martine. "Genetic mapping of restorer genes for cytoplasmic male sterility in Brassica napus using DNA markers." Thesis, McGill University, 1995. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=40147.
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DNA markers tightly-linked to nuclear fertility restorer genes for cytoplasmic male sterility (CMS) are valuable tools for breeders and researchers working with these genes. Two different targeting approaches were used to identify markers linked to the Rfp1 restorer gene for the pol CMS of canola (Brassica napus L.): nearly isogenic line (NIL) comparison and bulked segregant analysis. These methods were equally efficient in identifying markers linked to Rfp1; combining them allowed a targeting efficiency of 100% to be achieved. The efficiency of bulked segregant analysis was found to be limited by the inadvertent occurrence of shared homozygosity at specific chromosomal regions in the bulks, in contrast with the efficiency of NIL comparison which was limited by the occurrence of residual DNA from the donor cultivar at scattered sites around the genome of the NILs. Eleven DNA markers linked to the Rfp1 gene were identified, one of which perfectly co-segregates with Rfp1. The linkage group on which Rfp1 is localized contains 17 DNA markers. Two restorer genes of the pol CMS, Rfp1 and Rfp2, and a Rfn restorer gene of the nap CMS were found to be at least tightly linked to one another and may all reside at the same locus. A fourth restorer gene, the Rfo restorer for the ogu CMS, was, however, found to be unlinked to the other restorer genes. Different restorer genes for the nap CMS were found in the lines 'Westar-Rf and 'Karat'. A linkage map of the B. napus genome containing 146 markers organized into 23 linkage groups covering a total length of 850.2 cM was constructed from a BC$ sb1$ population. This map contains 63 loci previously localized on the B. napus genome through analysis of an F$ sb2$ population. Comparative analysis indicates that the total length of the BC$ sb1$-derived map is smaller than that of the F$ sb2$-derived map, which suggests that a reduction in recombination frequency is occurring in male gametes. The preferential use of two or three probe-
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陳文頌 and Man-chung Chan. "Genetic diversity and relationships of spiranthes sinensis, S. spiralis, and S. hongkongensis (orchidaceae) as revealed by RAPD andcpDNA markers." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 1997. http://hub.hku.hk/bib/B31214952.
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Vasemägi, Anti. "Evolutionary genetics of Atlantic salmon (Salmo salar L.) : molecular markers and applications /." Umeå : Dept. of Aquaculture, Swedish Univ. of Agricultural Sciences, 2004. http://epsilon.slu.se/s324.pdf.
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Dogan, Sukru Anil. "Reassessment Of Genetic Diversity In Native Turkish Sheep Breeds With Large Numbers Of Microsatellite Markers And Mitochondrial Dna (mtdna)." Master's thesis, METU, 2009. http://etd.lib.metu.edu.tr/upload/12610368/index.pdf.
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In the present study, within and among breed genetic variability in seven native Turkish sheep breeds (Akkaraman, Dagliç, Gö
kç
eada, ivesi, Karayaka, Kivircik and Morkaraman) were analyzed based on 20 microsatellite loci. For the analysis, various statistical methods such as Neighbor-Net, Factorial Correspondence Analysis (FCA) and Structure were used. High level of genetic variability within the Turkish breeds was observed. Gene pools of the breeds were visualized and found that they are highly overlapping with each other. As one of the reasons of this overlap, genetic exchange between the breeds was suggested. Dagliç
, claimed to be the ancestors of first domestic sheep in Anatolia, seemed to be the most admixed one. Yet Dagliç
, despite being the most introgressed one, still might be exhibiting its uniqueness. Observations implied that conservation practices concerning Dagliç
must be urgently revised. Results of the present study do not support previous observations about the genetic differentiation patterns of the breeds within Anatolia. Possible reasons of the discrepancies between the observations were discussed. Genetically extreme individuals can be identified by Structure, Assignment and FCA tests. These methods are found to be promising in establishing new relatively pure breeds or in saving the breeds from further genetic contamination. Genetically outlier individuals were shown not to exhibit any distinct morphological differences. Unknown band patterns were found by RFLP and SSCP of mtDNA Control Region and the individuals harboring those were sequenced. They were shown to belong to the common haplogroups A, B or C. No novel haplogroup was found.
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Baroni, Marco Giorgio. "Genetic analysis of non-insulin dependent diabetes mellitus (NIDDM) using DNA markers at candidate gene loci." Thesis, Queen Mary, University of London, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.294972.
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Chan, Man-chung. "Genetic diversity and relationships of spiranthes sinensis, S. spiralis, and S. hongkongensis (orchidaceae) as revealed by RAPD and cpDNA markers /." Hong Kong : University of Hong Kong, 1997. http://sunzi.lib.hku.hk/hkuto/record.jsp?B19324200.
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Berlin, Ingrid. "Tracking an elusive predator: Studying the Scandinavian lynx population by use of genetic markers." Thesis, Uppsala University, Department of Medical Biochemistry and Microbiology, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-8095.
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Abstract
Gaining accurate population information is crucial for the conservation and management of species. The National Monitoring Program for Large Carnivores monitors the Swedish lynx population (species Lynx lynx) by surveying family groups, non-invasive sampling and genetic analysis. Ten microsatellite regions were used as genetic markers to retrieve unique individual genotypes, through polymerase chain reactions (PCR) with specific primer-pairs and capillary-electrophoresis. Complete genotypes were matched using an internal database. The aim of this degree project was to show how monitoring of lynx through genetic analysis is carried out at the Department of Evolutionary Biology at Uppsala University, and to evaluate how effective these methods are and how they might be improved.
Even though most of the methods used were fairly robust and reproducible, non-invasive sampling and microsatellite analysis posed some problems regarding DNA quality and quantity, and increased the risks of certain genotyping errors. These risks might be worth taking though, as genetic analysis, in combination with field observations, gives a more comprehensive picture of the Swedish lynx population.
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Jordão, Junior Hamilton. "Desenvolvimento de um sistema baseado em marcadores moleculares de DNA do tipo microssatelites para identificação de variedades de cana-de-açucar." [s.n.], 2009. http://repositorio.unicamp.br/jspui/handle/REPOSIP/314755.
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Orientador: Gonçalo Amarante Guimarães PereiraDissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia
Made available in DSpace on 2018-08-13T04:49:03Z (GMT). No. of bitstreams: 1 JordaoJunior_Hamilton_M.pdf: 4716055 bytes, checksum: 76e45403d648d6e136baab29418a9ac0 (MD5) Previous issue date: 2009
Resumo: Melhoristas de cana-de-acucar tentam há muito tempo desenvolver um sistema confiavel de identificacao genetica baseado em marcadores moleculares para ajudar programas de melhoramento genetico. Alem disso, a União Internacional para a Proteção de Novas Variedades de Plantas (UPOV) tambem procura por um sistema que atenda os padrões de um teste DHE (Distinguibilidade, Homogeneidade e Estabilidade) podendo ser usado para apoiar ou substituir o processo de caracterização morfológica convencional em processos de registro de variedades. Um processo de descoberta e validacao de marcadores microssatelites usando um banco de dados de ESTs como unica fonte de sequencias de DNA foi estabelecido no trabalho e um sistema de identificação genetica baseada em marcadores microssatelites para cana-de-acucar foi desenvolvido para apoiar o melhoramento de variedades de cana-de-acucar e processos de registro de variedades. Um banco de dados de sequencias expressas (ESTs) com 352.122 sequencias foi avaliado para identificacao de motivos de microssatelite e 150 loci com alto polimorfismo observado in silico foram selecionados e validados em dois sistemas de resolução: Polyacrylamide Gel Electrophoresis (PAGE) e Sequenciador de DNA. Um conjunto de 10 loci foi selecionado de acordo com os valores de Conteudo de Informação Polimorfica (PIC) e qualidade visual do perfil cromatografico. A capacidade do sistema de discriminar individuos foi avaliada em 1.205 acessos de cana-de-acucar eespecies relacionadas. Uma combinação de tres loci foi suficiente para distinguir todos os acessos com pelo menos duas diferenças (alelos discriminatorios). A reprodutibilidade do sistema foi testada em um grande numero de amostras obtidas de diversos tecidos, origens geograficas distintas e plantulas de dois metodos de propagacao por cultura de tecido (meristema e calo), mostrando-se confiavel. O sistema de identificação genética preenche todos os requisitos para distinguibilidade, homogeneidade e estabilidade (teste DHE). O sistema pode tambem ter muitas aplicações uteis em programas de melhoramento de cana-de-acucar, tais como controle da identidade de acessos que compoem um banco de germoplasma, determinação de paternidade e rastreabilidade de clones em fase de seleção.
Abstract: Sugarcane breeders have been for long trying to develop a reliable molecular marker- based fingerprinting system that could aid their breeding programs. In addition, the International Union for the Protection of New Varieties of Plants (UPOV) has also been looking for such a system that, once it meets the standard of a DUS (Distinctness, Uniformity and Stability) test could be used to support or replace conventional morphological characterization used routinely to guarantee breeders property rights. A process of discovery and validation of microsatellites markers using EST database as the sole source for DNA sequences was established in this work and a microsatellite-based fingerprinting system for sugarcane was developed to support breeding of sugarcane varieties and property rights issues. An Expressed Sequence Tag (EST) database with 352,122 sequences was screened for microsatellite motifs and 150 loci with the highest polymorphism observed in silico were selected and validated in two fragment resolution systems, Polyacrylamide Gel Electrophoresis (PAGE) and automated DNA sequencer. A set of 10 loci was selected according to the Polymorphism Information Content (PIC) values and visual quality of chromatographic profiles. The capacity of the system to discriminate individuals was evaluated in 1,205 accessions of sugarcane and related species. A combination of three loci was sufficient to distinguish all accessions with the standard limit of at least two differences (discriminatory alleles). The reproducibility of the system was tested in large numbers of samples obtained from different tissues, distinct geographical origins, and plantlets from two tissue culture propagation methods (meristem and callus) and proved to be reliable. This fingerprinting system fulfills plant protection requirements for distinctness, uniformity, and stability (DUS test). The system may also have many useful applications in a sugarcane breeding program such as identification of mislabeled accessions in a germplasm bank, paternity determination and tracking of breeding populations.
Mestrado
Bioquimica
Mestre em Biologia Funcional e Molecular
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Fotinos, Tonya D. "Genetic Structure of the Florida Key Tree Cactus, Pilosocereus robinii, using Restriction Site associated DNA (RAD) markers." FIU Digital Commons, 2013. http://digitalcommons.fiu.edu/etd/914.
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Rare plant conservation efforts must utilize current genetic methods to ensure the evolutionary potential of populations is preserved. One such effort involves the Key Tree Cactus, Pilosocereus robinii, which is an endangered columnar cactus native to the Florida Keys. The populations have precipitously declined over the past decade because of habitat loss and increasing soil salinity from rising sea levels and storm surge. Next-generation DNA sequencing was used to assess the genetic structure of the populations. Twenty individuals representative of both wild and extirpated cacti were chosen for Restriction Site Associated DNA (RAD) analysis. Samples processed using the HindIII and NotIII restriction enzymes produced 82,382,440 high quality reads used for genetic mapping, from which 5,265 Single Nucleotide Polymorphisms (SNPs) were discovered. The analysis revealed that the Keys’ populations are closely related with little population differentiation. In addition, the populations display evidence of inbreeding and low genetic diversity.
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Sepulveda, Villet Osvaldo Jhonatan. "Population Genetic Structure and Biogeographic Patterns in the Yellow Perch Perca flavescens: An Analysis of Mitochondrial and Nuclear DNA Markers." University of Toledo / OhioLINK, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=toledo1321458463.
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Kongkiatngam, Prasert. "Genetic studies of red clover (Trifolium pratense L.) using morphological, isozyme and random amplified polymorphic DNA (RAPD) markers." Thesis, McGill University, 1995. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=29066.
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Genetic variation within and between two cultivars of red clover (Trifolium pratense L.), Essi from Europe and Ottawa from Canada was estimated using morphological, isozyme and random amplified polymorphic DNA (RAPD) markers. A total of 21 enzyme-coding loci with 43 alleles was detected using twelve enzyme systems. The mean number of alleles per locus was 1.81 in Essi and 1.67 in Ottawa. Nine 10-mer primers were used to assay 20 individuals from each cultivar for RAPD markers. Each primer gave from 7 to 20 amplified bands with an average of 14.8 bands per primer. High within-cultivar variation was observed in both cultivars using both isozyme and RAPD markers. The mode of inheritance of seven isozyme loci: Aat-2, Amy-1, Est-4, Est-7, Pgd-1, Pgd-2 and Skd-1, in red clover was verified. The genetic basis of banding patterns for 16 other isozyme loci: Aat-3, Adh-1, Dia-1, Dia-2, Dia-3, Est-1, Est-2, Gpi-2, Idh-1, Mdh-1, Mdh-2, Mdh-3, Mdh-4, Me-1, Me-2 and Pgm-2, was also postulated, based on the segregation patterns observed within cultivars. Two pairs of linked enzyme-coding loci, Est-4/Est-7 and Pgd-2/Skd-1, were found with joint segregation analysis. Estimates of genetic variability of 15 red clover cultivars from three different origins indicated that within-cultivar variation was much higher than between-cultivar variation. Allele frequencies of these isozymes could discriminate the five North American cultivars assayed, but they could not differentiate cultivars from Europe and Japan. The use of RAPD markers obtained from bulked samples was investigated for cultivar identification in red clover. Pooled samples were examined in order to minimize variation within cultivars. Twenty was found to be an appropriate number of red clover individuals per bulk for homogenizing genetic variation within cultivars. Fourteen 10-mer primers were used to amplify genomic DNA from combined leaf samples of 15 red clover cultivars from European, Japanese and North American origin
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Geleta, Mulatu. "Genetic diversity, phylogenetics and molecular systematics of Guizotia Cass. (Asteraceae) /." Alnarp : Department of Plant Protection Biology, Swedish University of Agricultural Sciences, 2007. http://epsilon.slu.se/200727.pdf.
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Qiu, Boxing. "DNA markers and genetics of resistance to cyst nematode and seed composition in soybean 'Peking' x 'Essex'." free to MU campus, to others for purchase, 1998. http://wwwlib.umi.com/cr/mo/fullcit-?p9924916.
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Bajracharya, Jwala. "Genetic diversity study in landraces of rice (Oryza sativa L.) by agro-morphological characters and microsatellite DNA markers." Thesis, Bangor University, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.273582.
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Debeila, Thipe Jan. "Characterisation of selected Culicoides (Diptera : Ceratopogonidae) populations in South Africa using genetic markers." Diss., University of Pretoria, 2010. http://hdl.handle.net/2263/25696.
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Culicoides (Diptera: Ceratopogonidae) are small (<3mm) blood feeding flies. These flies are biological vectors of viruses, protozoa and filarial nematodes affecting birds, humans, and other animals. Among the viruses transmitted those causing bluetongue (BT), African horse sickness (AHS) and epizootic haemorrhagic disease (EHD) are of major veterinary significance. Culicoides (Avaritia) imicola Kieffer, a proven vector of both AHS and BT viruses, is the most abundant and wide spread livestock-associated Culicoides species in South Africa. Field isolations of virus and oral susceptibility studies, however, indicated that a second Avaritia species, C. bolitinos Meiswinkel may be a potential vector of both BT virus (BTV) and AHS virus (AHSV). Differences in oral susceptibility, which are under genetic control, of populations from different geographical areas to viruses may be an indication of genetic differences between these populations, which may be the result of limited contact between these populations. A good knowledge of the distribution, spread and genetic structure of the insect vector is essential in understanding AHS or BT disease epidemiology. In the present study, an effort was made to gather field specimens of both C. imicola and C. bolitinos from different areas within their natural distribution in South Africa. The aim was to partially sequence two mitochondrial genes from these specimens and to analyse the sequence data making use of phylogenetic trees to clarify the genetic relationships between individuals or groups collected from geographically distinct sites. The two species were collected from four geographically separated areas in South Africa viz. Gauteng Province, Eastern Cape Province, Western Cape Province as well as the Free State Province. DNA was extracted from a total of 120 individual midges of the two Culicoides species using DNA extraction kits. Extracted DNA was analysed using PCR, sequencing as well as phylogenetic methods. A total of 117 mitochondrial DNA COI and 104 mitochondrial 16S ribosomal RNA CulidoidesDissertation (MSc)--University of Pretoria, 2010.Veterinary Tropical Diseases
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Gregonis, Daniel John. "The analysis of twelve forensic DNA genetic markers for Hardy-Weinberg and gametic phase disequilibrium for a Caucasian data base." CSUSB ScholarWorks, 1997. https://scholarworks.lib.csusb.edu/etd-project/1549.
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Coutts, Natalie June. "Investigating genetic diversity at neutral and adaptive DNA markers in the severly bottlenecked Southern white Rhinoceros (Ceratotherium simum simum)." Doctoral thesis, University of Cape Town, 2009. http://hdl.handle.net/11427/4252.
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Pérez-Espona, Silvia. "Genetic diversity and population genetic structure of red deer (Cervus elaphus) in the Scottish mainland, inferred by microsatellite markers and mitochondrial DNA control region sequences." Thesis, University of Edinburgh, 2006. http://hdl.handle.net/1842/11251.
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Despite the relatively small scale of the study area and the high dispersal capabilities of red deer, red deer on the Scottish mainland presented high levels of genetic diversity and significant population structure for both genetic markers, microsatellites (FST= 0.019; GST’ = 014) and mtDNA control region sequences (ΦST = 0.3483). The landscape genetics approach indicated that landscape features play an important role in contemporary gene flow of red deer on the mainland, with sea lochs, roads, mountain slopes and forests located along the Great Glen being responsible for most of the genetic differentiation in the study area. Sex-biased dispersal analyses, conducted using both genetic markers (microsatellites and mtDNA), revealed that male-biased dispersal was weak in the study area with male movements probably being predominant at a local scale (between neighbouring estates). In contrast, rarer long distance dispersal events which are more likely to be linked with colonisation of new areas were suggested to be predominantly female-biased. In terms of management, results from this study suggest that past management practices have not strongly affected the genetic integrity, genetic diversity and population genetic structure of red deer on the Scottish mainland. Phylogenetic analyses revealed that none of the red deer individuals included in this study presented a mtDNA haplotype from foreign deer despite the numerous introductions of foreign species of deer in the Scottish mainland such as wapiti (Cervus canadensis) or sika deer (Cervus nippon). Furthermore, only few localised individuals were found to have potentially descended from translocation events. Results from this study also support the continuation of current policies for the management of red deer man-made landscape features and to avoid further divisions of the group as the might not represent natural boundaries of populations.
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Jones, Donald Thomas. "A study of Hardy-Weinberg equilibrium, linkage equilibrium, and population structure in Hispanics using seven genetic markers." CSUSB ScholarWorks, 1997. https://scholarworks.lib.csusb.edu/etd-project/1478.
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Alamri, Sarah. "COMPARATIVE ANALYSIS OF SOYBEAN (GLYCINE MAX) ACCESSIONS USING INTER SIMPLE SEQUENCE REPEAT (ISSR) AND RANDOM AMPLIFIED POLYMORPHIC DNA (RAPD) MARKERS." Thesis, Laurentian University of Sudbury, 2014. https://zone.biblio.laurentian.ca/dspace/handle/10219/2201.
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Soybean (Glycine max) is an important crop in the world in terms of total production and usage. It is also among the least diverse species. The main objectives of the present study were 1) to determine differences between ISSR and RAPD marker systems in detecting genetic variation in soybeans and 2) to identify and characterize accession- diagnostic molecular markers in G. max accessions. Genomic DNAs from 108 G. max accessions from 11 different gene pools were analyzed using several ISSR and RAPD primers. The levels of polymorphic loci detected with the two marker systems were in general moderate and similar.. Overall, 82% of genetic distance values were above 0.40 based on ISSR analysis. However, RAPD data revealed that the accessions from different countries are closely related with 64% genetic distance values below 0.40. The dendrograms constructed with ISSR data revealed that the South Korean accessions formed an out-group while the RAPD analysis showed that accessions from Sweden were separate from the other 10 gene pools. One variety-diagnostic marker generated with ISSR 5 primer was identified in the accession Kao Chien Tao from China. This marker was cloned, and sequenced. Although RAPD and ISSR marker systems detected similar levels of genetic variability, they target different regions of the soybean genome, resulting in different clustering of the 11 gene pools indicating different genetic relatedness among them. This finding demonstrates the usefulness of both marker systems in assessing diversity and relatedness among Glycine max gene pools.
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Kerpauskaitė, Vilma. "Skirtingų paprastosios pušies (Pinus Sylvestris L.) lajos dalių sėklinių palikuonių genetinės įvairovės palyginimas." Master's thesis, Lithuanian Academic Libraries Network (LABT), 2012. http://vddb.laba.lt/obj/LT-eLABa-0001:E.02~2012~D_20120620_150922-88975.
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Magistro darbe lyginama vieno paprastosios pušies (Pinus sylvestris L.) klono skirtingų lajos dalių sėklinių palikuonių, augančių Višakio Rūdos bandomuosiuose želdiniuose, genetinė įvairovė remiantis DNR žymenimis ir kokybiniais bei kiekybiniais požymiais.
Darbo objektas – paprastosios pušies (Pinus sylvestris L.) sėklinių palikuonių želdiniai iš skirtingų lajos dalies sėklų (viršutinės, vidurinės, apatinės).
Darbo metodai – genetinė įvairovė tirta atliekant želdinių kiekybinių ir kokybinių požymių analizę bei jų DNR polimorfizmo tyrimą.
Darbo rezultatai. Fenotipinių požymių tyrimai parodė, kad 24 m amžiuje, viršutinės lajos dalies sėkliniai palikuonys pasižymi ženkliai didesniu išlikimu, bet esminiai nesiskiria savo kiekybinių ir kokybinių požymių įvairove nuo apatinės lajos dalies palikuonių. Gali būti, kad fenotipinių požymių įvairovei atsiskleisti trukdo nevienodas medžių išlikimas, kur esant mažesniam išlikimui, susidaro nevienodi tarpai tarp medžių, galėję įtakoti didesnę erdvinę įvairovę radialiniam prieaugiui. 6 chloroplasto DNR(cpSSR) lokusų DNR polimorfizmo tyrimai parodė, kad viršutinės lajos dalies sėklinių palikuonių genetinė įvairovė yra ženkliai didesnė nei vidurines ir apatinės lajos dalių sėklinių palikuonių. Iš 30 skirtingų cpSSR tipų (tėvinių genotipų) 18 buvo aptikti viršutinės lajos dalies palikuonyse, tuo tarpu vidurinėje dalyje – 8, o apatinėje - 10 .Visi 5 proc. savidulkinių individų aptikti tarp apatinės ir centrinės lajos dalies palikuonių (18 vnt.)... [toliau žr. visą tekstą]The genetic diversity of the progeny from different parts of Scots pine crown of a single clone by quantitative and qualitative traits and DNA polymorphism was investigated in the work of master science. Object of the work - 24 years old progeny from different parts of Scots pine crown of a single clone. The aim of the study - to compare the diversity of quantitative and qualitative traits and DNA polymorphism of24 years old progeny from different parts of Scots pine crown of a single clone by using cpSSR DNA markers. Methods of the work - Survival, stem diameter, stem straightness, flowering, cone yield, barktype,condition,the beginning of activegrowth and other parameters of the seedling progenies were evaluated. The genetic diversity was assessed at six cpDNA loci by the aid of cpSSRs. Study results. The results showed, that the survival of the progeny from the middle and the bottom of the crown was much lower than from the top. However, there were not any significant differences nor in the other traits neither between the variances of the progeny from the different parts of the crown. A reason could be that owing to low survival of the bottom and middle progeny, the remaining trees grew in a wider spacing and this uneven spacing between the treatments disturbed the comparison. cpSSR markers revealed much greater haplotype and allele diversity of the progeny from the top of the crown. Selfing rate was 5; background pollination 50; as much as 28 of the progeny from the... [to full text]
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Gonzalez, Malinda Wallentine. "Phylogenetic relationships of forest spiny pocket mice (Genus Heteromys) inferred from mitochondrial and nuclear markers with implications for species boundaries /." Diss., CLICK HERE for online access, 2005. http://contentdm.lib.byu.edu/ETD/image/etd777.pdf.
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Robbins, Marjorie. "The location of Tu on the genetic map of Lactuca sativa and the identification of random amplified polymorphic DNA markers flanking and tightly linked to Tu /." Thesis, McGill University, 1993. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=69684.
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In Lactuca sativa, the dominant gene Tu confers resistance to infection by turnip mosaic virus (TuMV). Tu and Dm5/8, a gene for resistance to Bremia lactucae, are linked in L. sativa. The area surrounding Dm5/8 on the genetic map of L. sativa contains restriction fragment length polymorphism (RFLP) and random amplified polymorphic DNA (RAPD) markers. The orientation of Tu relative to Dm5/8 was not known. Locating Tu would indicate which markers are on the map of lettuce close to Tu. To locate Tu on the L. sativa genetic map, F$ sb3$ families from recombinant F$ sb2$ in the Dm5/8 area of a cross between TuMV-resistant (Cobbham Green) and susceptible (Calmar) cultivars were inoculated with TuMV and phenotyped for Tu by indirect enzyme-linked immunosorbent assay. Polyclonal antibodies for immunodetection were produced using turnip mosaic virus coat protein expressed in E. coli. Phenotypic ratios within F$ sb3$ families were used to determine individual F$ sb2$ genotypes for Tu. With these genotypes, Tu was located on the genetic map of L. sativa relative to data present for Dm5/8 and surrounding markers, between OPM18 and OPY13. Using bulked segregant analysis, bulks created for the Dm5/8 locus were screened for genetic polymorphisms by the RAPD technique. Five new RAPD markers, UBC346, UBC517, UBC563, UBC599, and UBC675 were found linked to Tu after mapping relative to F$ sb2$ genotypes for Tu and other RAPD markers. The resulting three-point mapping information indicates that Tu is flanked by two markers, OPM18/OPL08 and UBC346, at respective genetic distances of 0.4 and 0.7 cM.
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Mwema, Hadija Saidi. "Forensic identification of six of Tanzanian populations using the extended haplotype markers." Thesis, University of the Western Cape, 2011. http://etd.uwc.ac.za/index.php?module=etd&action=viewtitle&id=gen8Srv25Nme4_2349_1325671867.
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The aim of the present study was to evaluate the power of discrimination and genetic (diversity) parameters in the Y chromosome extended haploytpe markers in populations of Tanzania for forensic and populations studies. Eleven Y chromosome extended haplotype markers were selected for this study, these includes Minimal haplotypes markers i.e. DYS19, DYS390, DYS391, DYS392, DYS393, DYS385a/b, DYS389I/II and two additional markers DYS438 and DYS439. Six populations of Tanzania were investigated under this study. These populations were selected based on the language family categoriesNiger Congo (Kuria and Sukuma), Nilo Saharan (Luo and Maasai) and Afro Asiatic (Iraqw and Alagwa).
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Oduor, Bonaventure Omondi Aman. "Ecology and population genetic structure of strains of Teretrius nigrescens (Coleoptera: Histeridae), predator of Prostephanus truncatus (Coleoptera: Bostrichidae) / Bonaventure Omondi Aman Oduor." Thesis, North-West University, 2009. http://hdl.handle.net/10394/5006.
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The larger grain borer (LGB) Prostephanus truncatus (Horn) is the most important pest of farm stored maize and cassava in Africa. This alien invasive species was introduced into the continent from Mesoamerica in the late 1970s and by 2008 had spread to at least 18 countries. In contrast to indigenous primary storage pests, LGB exists as on-farm and as wild populations, hence, sustainable control must target both environments. Biological control is especially attractive for wild populations to reduce early season grain store infestation, while cultural and chemical methods are useful to protect stored produce directly. Two populations of the predator Teretrius nigrescens Lewis were introduced into several African countries' as a biocontrol agent. It has shown long-term success and cost effective control in warm-humid areas. Control has however not been successful in cool and hot-dry zones. The aim of this study was to investigate the possible underlying genetic and ecological explanations for these observations and the possibility of joint use of molecular markers and ecological parameters in the development of sustainable control strategies. A 28-month baseline monitoring and recovery activity was done in from 2004 in five regions in Kenya along an east-westerly transect. Monitoring and live sample collection was also done in the original outbreak area in eastern Kenya. There was greater LGB flight activity in western Kenya (high potential maize production area) than the low potential areas. Very few T. nigrescens were recovered, solely in the eastern regions. LGB flight activity followed a seasonal pattern mostly related to changes in the relative humidity at 12:00, rainfall and dew point temperature but with a 3 - 4 week lag. A linear predictive model based on these factors predicted 27 % of the observed flight activity. The survival and predation of five strains of T. nigrescens were compared at eight temperature levels between 15 °C and 36 °C at low and high humidity. All the strains of T. nigrescens exerted a significant reduction of LGB population build-up between 21 °C and 33 °C with generally better performance under humid conditions. There was no evidence of T. nigrescens development at 15 °C. At 18 °C, T. nigrescens oviposition and development was observed but the effect on LGB did not differ significantly from the control. The KARI population was the least effective in preventing grain damage at lower temperatures, but performed better than other strains above 30 °C at low humidity conditions. There was no control at 18 °C and 36 °C under both high and low humidity conditions. Since the extent of genetic differentiation in T. nigrescens was unclear from prior studies, several molecular marker techniques were progressively used. The RAPD-PCR did not reveal any genetic diversity between geographical populations. A 1000bp region of the mitochondrial mtCOI gene revealed two distinct clades differing consistently at 26 segregating sites. The two clades can be identified by simple PCR-RFLP procedure using single or double sequential restriction with EcoR1, HincII, RsaI and DdeI digestion. However, the two lineages co-exist among the mid-altitude Central American populations. The internal transcribed spacer regions ITS1 and ITS2 with some neighbouring coding sequences of the ribosomal DNA were cloned and sequenced. The spacer regions were so variable in length and sequence between T. nigrescens and related Histeridae species that direct sequence alignment was not meaningful. Within T. nigrescens, there was intragenomic variability of the spacer regions mostly involving insertions and deletions of variable tandem repeat units predominantly within the ITS regions. The short flanking coding (18S, 5.8S and 21S) regions were conserved across populations and six other Histeridae species. There was no significant secondary structure variation of the ITS regions among populations of T. nigrescens. Twenty-four novel variable microsatellite markers were developed and tested on the Honduras populations. Alleles per locus ranged between two and twelve with observed heterozygosity between 0.048 and 0.646. Six loci deviated significantly from Hardy Weinberg Equilibrium and possibly had null alleles. The success of microsatellite amplification in outgroup species and variability of markers declined with an increase in the phylogenetic distance between the test species and T. nigrescens. Genotyping 432 individuals from 13 geographic populations revealed a comparatively higher genetic diversity in field populations. Partial isolation by distance and time was observed. Population bottlenecks were not detected, but recent expansion was evident in laboratory populations. Although five dominant genetic clusters were identified by Bayesian methods, meaningful hierarchical population structure was observed at between two and nine population groups (p < 0.01; 10,000 iterations). Biological control of the larger grain borer using T. nigrescens seems an important aspect of the sustainable integrated control approach of the pest. Ecological adaptations, appropriate release strategies and genetic diversity are all essential considerations in these efforts and could be responsible for the variable success already observed. There is some genetic differentiation between populations of T. nigrescens but, further studies would be necessary to ascertain the contribution of such diversity to its predatory performance. The effect of laboratory culturing in aggravating genetic drift should be accommodated to avoid loss of diversity during sampling, quarantine, rearing and release of the predator.Thesis (Ph.D. (Environmental Science))--North-West University, Potchefstroom Campus, 2009.
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Halldén, Christer. "Characterization and use of a multiplex PCR-based system random amplified polymorphic DNA /." Lund : Lund University, 1998. http://catalog.hathitrust.org/api/volumes/oclc/68945134.html.
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Karim, Sazzad. "Exploring plant tolerance to biotic and abiotic stresses /." Uppsala : Dept. of Plant Biology and Forest Genetics, Swedish University of Agricultural Sciences, 2007. http://epsilon.slu.se/200758.pdf.
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Hochschartner, Gerald. "Revealing the past : the potential of a novel small nucleolar RNA (snoRNA) marker system for studying plant evolution." Thesis, University of St Andrews, 2011. http://hdl.handle.net/10023/1695.
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Despite the existence of various molecular marker systems there are still limitations in distinguishing between closely related species based on molecular divergence, especially when hybridization events have occurred in the past. The characterisation of plant small nucleolar RNA (snoRNA) genes and their organisation into multigene clusters provides a potential nuclear marker system which could help in resolving the phylogenetic history of plants and might be applicable in DNA barcoding. Using closely and distantly related Senecio species, I investigated a combination of fragment length and sequence variation of snoRNA genes/snoRNA gene clusters to assess the utility of this marker system for barcoding and resolving species relationships. SnoRNA gene and gene cluster sequences identified in Arabidopsis thaliana were used to find homologues in other species and subsequently used for the design of universal primers. Most of the universal primer pairs designed were successful in amplifying snoRNA fragments in most Senecio species and fragment length variation between and within species could be detected. Furthermore, the combination of some fragment length datasets produced by different primer pairs enabled the separation of species and the detection of reticulate evolution indicating a high potential of snoRNA gene/gene cluster fragment length polymorphisms (SRFLPs) for phylogenetic reconstructions in Senecio and other plant genera. Most of the examined gene clusters showed a similar gene order in Senecio and Arabidopsis. However, the majority of these clusters appeared to exhibit more copies in Senecio, some of which were distinguishable by a combined sequencing/fragment profiling approach, and shown to be putative single copy regions with the potential to be used as co-dominant markers. However, a high number of paralogues and possible differences in copy number between species excludes these regions from being used in DNA barcoding. This is because specific primers would have to be developed for specific copies which would preclude development of a universal application for barcoding. None of the regions showed enough sequence variation to delimit distinctly closely related Senecio species and were therefore also considered to be unsuitable for DNA barcoding. Although most snoRNA genes and gene clusters might be inapplicable for DNA barcoding, they are likely to be valuable for phylogenetic studies of species groups, genera and families. On this scale, specific primers might act universally and the number of paralogous copies is likely to be equal across the species group of interest.
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Carmine, Andrea. "On Parkinson's disease and schizophrenia : case control studies, cellular localization and modelling of candidate genes /." Stockholm, 2003. http://diss.kib.ki.se/2003/91-7349-671-5.
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Canivell, Fusté Silvia. "The association of DNA methylation patterns in TCF7L2 and GIPR genes with Type 2 Diabetes." Doctoral thesis, Universitat de Barcelona, 2014. http://hdl.handle.net/10803/284198.
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The incidence of type 2 diabetes mellitus (T2D) is increasing worldwide. There are several explanations to this fact, such as the increased prevalence of obesity, population’s ageing, and the lack of physical activity that is practised. However, not all obese and sedentary individuals become type 2 diabetic. Beyond a certain genetic susceptibility and a determined environment, some people will become diabetic, whereas others will not. Recent discoveries in the field of epigenetics have brought an insight in the molecular mechanisms underlying the interaction between environment and genome. Indeed, it is believed that specific changes in the epigenome are associated with the onset and/ or the progression of disease processes such as cancer or diabetes. TCF7L2 is the susceptibility gene for T2D with the largest effect on disease risk that has been discovered to date. However, the mechanisms by which TCF7L2 contributes to the disease remain largely elusive. On the other hand, GIP action in T2D patients is altered. As said above, epigenetic mechanisms, such as changes in DNA methylation patterns, might have a role in the pathophysiology of T2D. In this study, we hypothesized that methylation changes could be present in GIP receptor of T2D patients and in the TCF7L2 gene. This study aimed to assess the differences in DNA methylation profile of GIPR and TCF7L2 promoters between T2D patients and age- and Body Mass Index (BMI)-matched controls. We included 93 T2D patients (cases) that were uniquely on diet (without any anti-diabetic pharmacological treatment). We matched one control (with oral glucose tolerance test negative, non diabetic), by age and BMI, for every case. Cytokines and hormones were determined by ELISA. DNA was extracted from whole blood and DNA methylation was assessed using the Sequenom EpiTYPER system.
Our results showed that type 2 diabetic patients were more insulin resistant than their matched controls (mean HOMA IR 2.6 vs 1.8 in controls, P<0.001) and had a poorer beta-cell function (mean HOMA B 75.7 vs. 113.6 in controls, P<0.001). Fasting adiponectin was lower in T2D patients as compared to controls (7.0±3.8 µgr/mL vs. 10.0±4.2 µgr/mL). Levels of IL 12 in serum were almost double in T2D patients (52.8±58.3 pg/mL vs. 29.7±37.4 pg/mL). We found that GIPR promoter was hypomethylated in T2D patients as compared to controls. In addition, HOMA-IR and fasting glucose correlated negatively with mean methylation of GIPR promoter, especially in T2D patients. With reference to the TCF7L2 promoter, results showed that 59% of the CpGs analyzed in TCF7L2 promoter had significant differences between type 2 diabetic patients and matched controls. In addition, fasting glucose, HOMA-B, HOMA-IR, total cholesterol and LDL-cholesterol correlated with methylation in specific CpG sites of TCF7L2 promoter. After adjustment by age, BMI, gender, physical inactivity, waist circumference, smoking status and diabetes status uniquely fasting glucose, total cholesterol and LDL-cholesterol remained significant.
This case-control study confirms that newly diagnosed, drug-naïve T2D patients are more insulin resistant and have worse β cell function than age- and BMI-matched controls, which is partly related to changes in the insulin-sensitizing metabolites (adiponectin), in the proinflammatory profile (IL12) and we suggest in the methylation pattern of GIPR. Moreoever, newly diagnosed, drug-naïve type 2 diabetic patients display specific epigenetic changes at the TCF7L2 promoter as compared to age- and BMI-matched controls. Methylation in TCF7L2 promoter is further correlated with fasting glucose in peripheral blood DNA, which sheds new light on the role of epigenetic regulation of TCF7L2 in T2D.
Our study provides novel findings on GIPR and TCF7L2 promoters methylation profile which may improve our ability to understand type 2 diabetes pathogenesis.En nuestra investigación, se plantea la hipótesis que los pacientes diabéticos tipo 2 se diferencian respecto a sujetos no diabéticos de misma edad e índice de masa corporal (IMC) en patrones de metilación específicos que podrían implicar cambios en la expresión génica en los tejidos diana implicados en la fisiopatología de la diabetes tipo 2. En vista de la interacción entre el medio ambiente y la genética, y, que los patrones de metilación pueden cambiar en respuesta a los factores ambientales, se deduce que los patrones de metilación relacionados con la diabetes estarían presentes en los genes clave implicados en la fisiopatología de la diabetes tipo 2, como los genes TCF7L2 y GIPR. Como el patrón de metilación podría influir en la expresión génica, estudiamos la región promotora de los genes seleccionados. Por último, como las marcas epigenéticas pueden ser detectadas a partir de tejidos fácilmente accesibles, se estudiaran las marcas de metilación en el ADN de la sangre total en los dos grupos de sujetos. La primera parte del trabajo demuestra que los pacientes con diabetes tipo 2 de reciente diagnóstico tienen una función de las células β alterada y son más insulino- resistentes que los controles apareados por edad e IMC. Estas diferencias en la función de las células β y la resistencia a la insulina están relacionadas con diferencias en los perfiles de adipoquinas así como metabolitos inflamatorios, que podrían reflejar parte de los mecanismos subyacentes que conducen a la diabetes tipo 2 manifiesta. Posteriormente, hemos demostrado la presencia de alteraciones epigenéticas en pacientes con diabetes tipo 2 en comparación con controles emparejados por edad e IMC en ciertas regiones del genoma que han sido previamente vinculados a la diabetes tipo 2 y a la hiperglucemia, como los genes TCF7L2 y GIPR. Estos nuevos resultados aclaran la visión actual de la asociación entre las alteraciones epigenéticas y regiones genómicas de riesgo conocido para la diabetes tipo 2 y se abren nuevas líneas de investigación sobre este tema.
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Khan, Abdul Rehman. "Short term response of European wheat populations to contrasted agro-climatic conditions : a genetic analysis and first step towards development of epigenetic markers in earliness gene VRN-A1." Phd thesis, Université Paris Sud - Paris XI, 2013. http://tel.archives-ouvertes.fr/tel-00980832.
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Biodiversity provides the raw material for evolution and adaptation of populations and species. In agricultural biodiversity, the within-population genetic diversity is of major importance. On one hand, it can provide a buffering effect against the year-to-year variation of climate or biotic pressures and on the other hand diversity serves as a resource for the population to respond to selective pressures due to specific local conditions, thus allowing for local adaptation, particularly in the case where a population is introduced into a new location. Due to its wide geographic distribution indicating a high adaptiveotential and its socio-economic importance, wheat was chosen as model crop in this study. Flowering time is a major adaptive trait which has allows wheat to grow over a wide range of ecological and climatic conditions. This PhD study was designed to gain insights about the influence of within population diversity on the short term response of populations to contrasting agro-climatic conditions by studying the genetic, epigenetic and phenotypic variation. But due to the lack of prior existence of epigenetic markers, this thesis study is divided of two parts: In the first part, European wheat populations coming from a set of seven farmer and one modern varieties, each of which was grown on seven farms (distributed across Europe) for three years, were used to study their short term response to contrasting agro-climatic conditions in Europe by analysing their phenotypic and genotypic variations. For the second part the effect of vernalization on the DNA methylation profile of theVRN-A1 gene in winter wheat was studied as a first step towards the development for the epigenetic marker in this gene.The results from the first part of the study revealed that conservation history of these farmer varieties strongly influenced the genetic diversity and fine genetic structure. Ex situ conserved farmer varieties showed low genetic diversity and simpler structure whereas in situ conserved farmer varieties and mixtures revealed higher level of genetic diversity and complex genetic structure. Genetic and phenotypic spatio-temporal differentiation depending upon the level of diversity and structural complexity of the farmer variety was observed. The traditional varieties tend to become more differentiated than the modern variety arguing in favour of use of these diverse traditional (farmer) varieties in organic and low input agriculture systems. Interestingly, a significant phenotypic differentiation for varieties with very low genetic diversity has also been observed in this study, which gives indication of a possible role of epigenetic variation in the process of evolution.From the second part of the study (effect of vernalization on the DNA methylation profile of the VRN-A1 gene), it was found that in addition to the detection of gene body methylation across the VRN-A1 gene, we identified a region within intron 1 that shows significant increase in DNA methylation in response to vernalization treatment that is positively correlated with the gene expression. Although the role of this shift in gene regulation is still unclear due to time limitations in the thesis and the small number of genotypes analysed, this study will provide a good material towards future identification of new epialleles and the development of epigenetic markers to study the epigenetic variability of these populations.This study at large provides useful knowledge on the understanding of farmers' varieties evolutionary response to be used in the development of different breeding and conservation approaches for organic agriculture, taking into consideration of the importance of within population diversity, to satisfactorily address the problems of organic agriculture.
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Gunnar, Erika. "Characterization of the genetic basis in two cases of abetalipoproteinemia reveals two novel mutations." Thesis, Linköping University, Department of Physics, Chemistry and Biology, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-58620.
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BACKGROUND: Abetalipoproteinemia (ABL) is a rare autosomal recessive disorder caused by mutations in the gene coding for microsomal triglyceride transfer protein (MTTP).
AIM: To characterize the genetic basis of ABL in two unrelated patients.
RESULTS: In the first patient, the substitution c.1911C>T in exon 12 of the MTTP gene, resulting in the protein substitution p.P552L, was discovered using mutation screening. The parents are heterozygous and the proband is a homozygous carrier of this substitution. Using restriction fragment length polymorphism (RFLP), 100 control subjects were analyzed and none carried the substitution indicating that it is a novel MTTP mutation. Sequencing of the other ABL patient showed that the proband carried a homozygous single base insertion, at position c.2342IVS16+2-3insT, located at the donor splice-site of intron 16 resulting in skipping of exon 16 and truncation of the protein. The proband's mother is heterozygous for the insertion while the father does not carry the insertion. Multiplex ligation-dependent probe amplification (MLPA) did not identify any deletion encompassing exon 16 in the proband, father or mother. Nonpaternity was excluded using polymorphic markers from several chromosomes. Haplotype analysis using markers spanning chromosome 4 revealed heterodisomy (two homologous chromosomes) of 4p and the distal part of 4q, and isodisomy (duplication of one chromosome) of 4q12-4q26.
CONCLUSION: These data show that the cause of ABL in one of the patients is a missense mutation, p.P552L, while the cause of ABL in the other patient is due to uniparental disomy, probably resulting from non-disjunstion in meiosis I.
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Cardena, Mari Maki Síria Godoy. "Avaliação da relação entre haplogrupo mitocondrial e ancestralidade genômica no desenvolvimento de insuficiência cardíaca em amostra brasileira." Universidade de São Paulo, 2013. http://www.teses.usp.br/teses/disponiveis/5/5160/tde-18102013-151616/.
Full textAbstract:
As doenças cardiovasculares lideram as causas de morte em vários países, inclusive no Brasil, sendo a insuficiência cardíaca (IC) uma das enfermidades mais frequentes. Estudos epidemiológicos e de genética têm demonstrado associações entre a origem étnica dos indivíduos e o desenvolvimento de diversas doenças cardiovasculares. O presente estudo teve como objetivo avaliar a relação entre haplogrupos mitocondriais e ancestralidade genômica no desenvolvimento da IC. Foram avaliados 503 pacientes com IC e 188 controles saudáveis. Os haplogrupos mitocondriais foram obtidos pela análise da região controle do DNA mitocondrial (mtDNA) e o estudo de ancestralidade genômica foi realizado pela análise de 48 marcadores autossômicos informativos de ancestralidade (AIMs) tipo INDEL. As análises estatísticas foram realizadas com o uso de regressão logística, construção de curvas de Kaplan-Meier e utilizando o método estatístico de log-rank (Mantel-Cox). Os resultados dos AIMs evidenciaram contribuições semelhantes de ancestralidade genômica entre os grupos de pacientes e controles, evidenciando a não estratificação populacional da amostra. A comparação dos haplogrupos mitocondriais entre os dois grupos revelou uma associação dos haplogrupos africanos com risco aumentado (p=0,015; OR 1,56) para o desenvolvimento da IC, enquanto que os haplogrupos ameríndios foi associado a um menor risco (p=0,043; OR 0,71). As análises realizadas apenas dentro do grupo de pacientes revelaram que 74,6% dos indivíduos se autodeclararam como brancos. As etiologias encontradas com maior frequência na nossa amostra foram a hipertensiva (28,6%) e a isquêmica (28,4%). A análise de mtDNA evidenciou que pacientes pertencentes aos haplogrupos africano apresentaram risco aumentado para o desenvolvimento da IC nas etiologias chagásica (p=0,012; OR 2,32) e hipertensiva (p=0,003; OR 2,05). Evidenciou também que pacientes dos haplogrupos africanos, principalmente da etiologia isquêmica, desenvolveram IC mais cedo que os demais, e que os pacientes com esses haplogrupos da etiologia valvar apresentaram maior sobrevida no período avaliado. A análise dos AIMs demonstrou que, na etiologia hipertensiva, a maior contribuição da ancestralidade genômica africana conferiu risco aumentado (p=0,002; OR 6,07), enquanto que a maior contribuição de ancestralidade genômica europeia conferiu risco diminuído (p=0,001; OR 0,16) para o desenvolvimento da IC; os pacientes com maior contribuição de ancestralidade genômica ameríndia apresentaram maior sobrevida no período de 4 anos. O uso de marcadores autossômicos e do DNA mitocondrial fornece estimativas mais precisas da ancestralidade de um indivíduo e/ou população, enquanto que a autodeclaração de cor de pele fornece indiretamente informações importantes sobre aspectos socioeconômicos e culturais. Assim, seria interessante a utilização, especialmente em populações miscigenadas, de uma construção tridimensional de análise, que poderia fornecer dados mais informativos e complementares em estudos de associação entre etnia e fenótipos e/ou doenças complexasCardiovascular diseases are the leading cause of death in many countries, including Brazil, being the heart failure (HF) one of the most common diseases. Epidemiological and genetic studies have shown associations between the ethnic origin of individuals and the development of various cardiovascular diseases. The aim of this study was to evaluate the relationship between mitochondrial haplogroups and genomic ancestry in the development of HF. We evaluated 503 patients with HF and 188 healthy controls. The mitochondrial haplogroups were obtained by analysing the control region of mitochondrial DNA (mtDNA) and the study of genomic ancestry was conducted by the analysis of 48 autosomal ancestry informative markers (AIMs) INDEL type. Statistical analyzes were performed using logistic regression, construction of the Kaplan-Meier and using the log-rank test (Mantel-Cox). The results of AIMs showed similar contributions of genomic ancestry among the patients and controls groups, indicating no population stratification of the sample. Comparing mitochondrial haplogroups between the groups, we observed that african haplogroups show increased risk (p=0.015, OR 1.56) of development of the HF, while ameridian haplogroup was associated with a reduced risk (p=0.043, OR 0.71). The analysis carried out only within the group of patients showed that 74.6% of individuals self-declared as white. The etiologies found with greater frequency in our sample were hypertension (28.6%) and ischemic (28.4%). Analysis of mtDNA showed that patients belonging to african haplogroup have increased risk of the development of HF in chagasic (p=0.012, OR 2.32) and hypertensive etiologies (p=0.003, OR 2.05). It also showed that patients of african haplogroups, specially of ischemic etiology, developed HF earlier than others, and the patients with this haplogroup of valvular etiology had better survival in the study period. AIMs analysis showed that in hypertensive etiology, the major contribution of african genomic ancestry conferred increased risk (p=0.002, OR 6.07), while the major contribution of european genomic ancestry conferred decreased risk (p=0.001, OR 0 16) to the development of HF; patients with higher contribution of amerindian genomic ancestry had better survival within 4 years. The use of autosomal markers and mtDNA provides more accurate estimates of ancestry of an individual and/or population, while the self-declared ethnicity, indirectly provides important information about socioeconomic and cultural aspects. Thus, it would be interesting to use, especially in admixed populations, the construction of a three-dimensional analysis, which could provide more informative and complementary data in studies of association between ethnicity and phenotypes and/or complex diseases
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Silva, Iede Hercília Emerenciano Ferreira da. "Estudo da freqüência haplotípica dos marcadores microssatélites ligados ao cromossomo X, DXS7424, DXS101, DXS10079, DXS10075 e DXS10074 na população de Alagoas." Universidade Federal de Alagoas, 2008. http://repositorio.ufal.br/handle/riufal/929.
Full textAbstract:
The STR markers linked to the X chromosome can be used for complement the analysis of autosomal markers, especially in complex cases of kinship testing, in cases of post-morten identification and in paternity testing, when the disputed child is a girl. The aim of this work was investigate five STR X-chromosome markers (DXS10079, DXS10074, DXS10075, DXS7424 and DXS101) in the population of Alagoas, Brazil and analyze their frequencies for forensic purposes. The sample was composed of 404 unrelated individuals, 203 males and 201 females. The DNA was extracted using Chelex procedure and amplification was performed by PCR in a pentaplex system and the fragments were separated by capillary electrophoresis. For the studied STR markers, it was calculated the allele and haplotype frequencies, the observed and expected Heterozygosity values, the Hardy Weinberg equilibrium (HWE), the genetic diversity, the Mean Exclusion Chance of trios involving daughters (MECT) as well as in father/daughter duos (MECD). Also, it was calculated Power of Discrimination in males (PDM) and in females (PDF) and the Polymorphism Information Content (PIC). The forensic efficiency values demonstrate that DXS101 is a highly informative marker, followed by DXS10074, DXS10079, DXS7424 and DXS10075. The polymorphism information content ranged from 0.7470 to 0.8858. For the pentaplex evaluated, the combined values of PDM and PDF were 0, 9998947 and 0, 9999998, respectively and the combined MEC in trios involving daughters and in father/daughter duos were 0,999817 and 0,998042, respectively. No deviations from the Hardy Weinberg equilibrium were observed. We concluded that the five ChrX STRs analyzed are highly informative markers for kinship testing and constitute a powerful tool for forensic practice in our population.Fundação de Amparo a Pesquisa do Estado de Alagoas
Os marcadores STRs ligados ao cromossomo X podem ser utilizados para complementar as análises de marcadores autossômicos, especialmente em casos complexos de vínculo genético, em casos de identificação post-morten e em testes de paternidade, quando a criança analisada é uma menina. O objetivo desse trabalho foi investigar cinco marcadores STRs do cromossomo X (DXS10079, DXS10074, DXS10075, DXS7424 e DXS101) na população de Alagoas, Brasil, e analisar suas freqüências para propósitos forenses. A amostra foi composta de 404 indivíduos não aparentados, sendo 203 do sexo masculino e 201 do sexo feminino. O DNA foi extraído através do método Chelex-100 e a amplificação foi realizada por PCR em um sistema pentaplex, sendo os fragmentos separados por eletroferese de capilar. Para os marcadores STRs estudados, foram calculadas as freqüências alélicas e haplotípicas, Heterozigozidade esperada e observada, Equilíbrio de Hardy Weinberg (HWE), diversidade genética, Chance Média de Exclusão (MEC) em trios envolvendo filhas e em duplas de pai/filha. Também foram calculados Poder de Discriminação em homens (PDM) e mulheres (PDF) e Conteúdo de Informação Polimórfica (PIC). Os parâmetros forenses investigados demonstram que o STR DXS101 é o marcador mais informativo, seguido por DXS10074, DXS10079, DXS7424 e DXS10075. O Conteúdo de Informação Polimórfica variou de 0.7470 a 0.8858. Para o sistema pentaplex investigado, os valores combinados de PDM e PDF foram de 0,9998947 e 0, 9999998, respectivamente e o MEC combinado em trios envolvendo filhas e em duplas pai/filha foi de 0,999817 e 0, 998042, respectivamente. Nenhum desvio do Equilíbrio de Hardy Weinberg foi observado. Concluímos que os cinco marcadores analisados são altamente informativos para testes de parentesco e constituem uma poderosa ferramenta genética para a prática forense em nossa população.