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Bitalo, Daphne Nyachaki. "Implementation of molecular markers for triticale cultivar identification and marker-assisted selection." Thesis, Stellenbosch : Stellenbosch University, 2012. http://hdl.handle.net/10019.1/71670.
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Thesis (MSc)--Stellenbosch University, 2012.Triticale is an amphidiploid that consists of wheat (A and B) and rye (R) genomes. This cereal is fast becoming important on a commercial basis and warrants further assessment for the better management and breeding of the hybrid. The assessment of the genetic diversity among the wheat and rye genomes within triticale can be obtained by using molecular markers developed in both donor genomes. Simple sequence repeats markers (SSRs) and amplified fragment length markers (AFLPs) have been previously used to assess the genetic diversity among triticale lines. SSRs are highly polymorphic markers that are abundant and which have been shown to be highly transferable between species in previous studies while AFLP markers are known to generate plenty of data as they cover so many loci. Thus, the aim of this study was to develop a marker system suitable to assess the genetic diversity and relationships of advanced breeding material (and cultivars) of the Stellenbosch University’s Plant Breeding Laboratory (SU-PBL). Therefore, both AFLP and SSR markers were initially analysed using eight triticale cultivars (with known pedigrees) to facilitate cultivar identification. Fourty-two AFLP primer combinations and 86 SSR markers were used to assess the genetic diversity among the Elite triticale cultivars. The AFLP primer combinations generated under average polymorphism information content (PIC) values. Furthermore, these markers generated neighbour-joining (NJ) and unweighted pair group method with arithmetic average (UPGMA) dendograms that displayed relationships that did not correspond with the available pedigree information. Therefore, this marker system was found not to be suitable. A set of 86 SSRs previously identified in both wheat and rye, was used to test the genetic diversity among the eight cultivars. The markers developed in wheat achieved 84% transferability while those developed in rye achieved 79.3% transferability. A subset of SSR markers was able to distinguish the cultivars, and correctly identify them by generating NJ and UPGMA dendograms that exhibited relationships that corroborated the available pedigree data. This panel of markers was therefore chosen as the most suitable for the assessment of the advanced breeding material. The panel of seven SSR markers was optimised for semi-automated analysis and was used to screen and detect the genetic diversity among 306 triticale entries in the F6, Senior and Elite phases of the SU-PBL triticale breeding programme. An average PIC value of 0.65 was detected and moderate genetic variation was observed. NJ and UPGMA dendograms generated showed no clear groupings. However, the panel of markers managed to accurately identify all cultivars within the breeding program. The marker panel developed in this study is being used to routinely distinguish among the advanced breeding material within the SU-PBL triticale breeding programme and as a tool in molecular-assisted backcross.
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von, Ruhland Christopher John. "The molecular basis of modern marker chemistry." Thesis, Cardiff University, 2011. http://orca.cf.ac.uk/22318/.
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This thesis focuses on empirical investigations and refinements of immunohistochemical marker chemistry to gain insights into the design of novel markers for light and electron microscopy. In Chapter 2, incorporation of d-block metals into polymerised biphenyl-3,3′,4,4′-tetramine (polyDAB) identified complexes of Ni(II), Pt(II), Pt(IV) and Au(III) to be powerful catalysts of silver reduction from physical developers. Na2S(aq) treatment increased the range and activity of catalytic complexes, allowing previously invisible immunohistochemical deposits of polyDAB to be clearly seen in diagnostically relevant samples. Chapter 3 refined this technique by manipulating reagent concentrations whilst suppressing tissue argyrophilia, increasing immunohistochemical sensitivity by an order of magnitude. Marker deposition and thus amplification, was dependent on conjugate quality and coupling method. In Chapter 4, scanning and transmission electron microscopy identified 8 d-block metals that increased the electron opacity of polyDAB, including W(VI), Os(VIII), Pt(II) and Au(III). The majority were detectable by energy dispersive X-ray analysis (EDX), but were present in insufficient quantities for use in analytical electron microscopical tomography (AEMT). In Chapter 5, immunohistochemical polymerisation of halogenated aromatic diamines and bis-diamines as AEMT markers was investigated. The 16 compounds studied produced deposits of varying properties and compositions, morphological criteria identifying those of 1,2-diamino-4-bromobenzene and 1,2-diamino-4,5-diiodobenzene as suitable candidates; EDX indicated that the latter might be applicable to AEMT. Chapter 6 investigated silver deposition from a physical developer by photoconversion. Photo-excitation of immunofluorescently-stained tissue sections in the presence of physical developer caused selective silver deposition at immunopositive sites, a novel method that might find application in AEMT. In Chapter 7, characterisation of polyDAB revealed a molecular weight range of 600 to over 100,000; IR spectra were consistent with an indamine- or phenazine-like polymer. Poor solubility restricted further characterisation. In Chapter 8, additional applications of halogenated compounds were investigated and results suggested potential applications in biological research and diagnosis.
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Jessup, Russell William. "Molecular tools for marker-assisted breeding of buffelgrass." Texas A&M University, 2005. http://hdl.handle.net/1969.1/2656.
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The increasing availability of molecular tools is facilitating marker-assisted
selection (MAS) in plant improvement programs. The objectives of this research were
to: 1) populate the framework buffelgrass genome map with additional molecular
markers, 2) develop polymerase chain reaction (PCR)-based markers from selected,
informative restriction fragment length polymorphism (RFLP) markers on the
buffelgrass genome map, and 3) increase marker resolution near the locus conferring
apomixis (PApo1). Buffelgrass [Pennisetum ciliare (L.) Link syn. Cenchrus ciliaris L.]
(2n=4x=36), a highly polymorphic, apomictic, perennial forage grass, is well-suited for
genetic linkage analyses. One hundred and seventy one probes from an apomictic,
spikelet-specific, complementary deoxyribonucleic acid (cDNA) library and 70
expressed sequence tag simple sequence repeats (EST-SSRs) from apomictic pistil
cDNAs were evaluated and added to the framework buffelgrass genome map. The
improved linkage map contains 851 markers from 11 grass species and covers
approximately 80-85% of the buffelgrass genome. Two RFLPs from the buffelgrass
genome map were converted to PCR-based markers for both the identification of hybrids and quantification of sexual versus apomictic reproduction. A gel-free, high-throughput
technique was developed to analyze these markers directly in 96-well plates. Five
additional markers were placed onto the buffelgrass linkage group with the PApo1
apomixis locus through comparative mapping of candidate orthologs from the sorghum
genome map and bulked-segregant analysis of amplified-fragment-lengthpolymorphisms
(BSA-AFLP). Increasing the mapping population size did not increase
map resolution in the PApo1 region. Association mapping revealed that the
recombination suppression near PApo1 is moderate and would complicate comparative
map-based cloning efforts of the orthologous region in sorghum.
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Ozen, Ilknur. "Neurogenin2, a molecular marker of postnatal hippocampal neurogenesis." Thesis, University of Cambridge, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.612424.
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Santos, Nadine Castelhano. "SARP2 as molecular marker of human sperm morphology." Master's thesis, Universidade de Aveiro, 2011. http://hdl.handle.net/10773/5800.
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Mestrado em Biologia Aplicada - Biologia Molecular e CelularA fosforilação proteica resulta de um equilíbrio entre fosfatases e quinases constituindo o principal regulador da maioria dos mecanismos existentes nos sistemas biológicos. Muitas doenças (cancro, diabetes, doenças neurodegenerativas, infertilidade, etc.) estão associadas à disrupção deste equilíbrio levando a mudanças nas actividades enzimáticas das proteínas fostatase e quinase. A proteína fosfatase 1 (PP1) é a principal fosfatase serina/treonina sendo ubíqua e altamente conservada nos eucariotas. A PP1 controla várias funções, tais como, a divisão celular, a transcrição, a neurotransmissão, a mobilidade dos espermatozóides, entre outras. A fosforilação proteica é uma das formas de os espermatozóides adquirirem funcionalidade, sendo a proteína PP1γ2 a isoforma mais fortemente enriquecida. Assim, no interior do espermatozóide podemos encontrar a PP1γ2 associada ao comprimento total da cauda e à região equatorial da cabeça, sugerindo uma possível função na mobilidade e reacção acrossómica, respectivamente. Existem inúmeras proteínas que interagem com a PP1γ2 que têm vindo a contribuir para a compreensão do seu papel nas funções fisiológicas do espermatozóide. Apesar de existirem outros, nesta tese, o complexo que serviu de ponto de partida foi o complexo SARP2/PP1γ2. Este complexo inclui uma nova proteína derivada de splicing, primeiramente descrita por Browne e os seus colaboradores em 2007, contendo três isoformas. Nesta tese foi usada a isoforma SARP2. O complexo foi encontrado fortemente enriquecido em espermatozóides e esta descoberta levou a estudos futuros com vista a descobrir a sua função fisiológica no espermatozóide. Usando a proteína SARP2 como um possível marcador molecular procurou-se verificar se era possível distinguir os espermatozóides em normais ou anormais. Considerando a actual necessidade em desenvolver novas técnicas de diagnóstico da infertilidade masculina, a descoberta de biomarcadores pode apresentar uma possível via, especialmente devido à perda de valor da avaliação dos parâmetros de um espermograma. No presente trabalho descobriu-se uma localização sub-celular no espermatozóide diferente da descrita anteriormente. O padrão de expressão da SARP2 é muito variável existindo catorze padrões diferentes do padrão normal encontrado. Contudo não foi possível confirmar com total certeza de que tínhamos um putativo marcador molecular. O presente trabalho fornece dados suficientes para que no futuro se possa realizar um plano experimental optimizado, com mais voluntários, representativo da população Portuguesa. Por fim, é necessário complementar o estudo com testes paralelos (fragmentação do DNA, ROS, etc.) que permitam avaliar a normalidade ou não de um espermatozóide em contraponto com a observada no estudo.
Protein phosphorylation, is the result of a balance between phosphatases and kinases being the key regulator for the major mechanisms in biological systems. Many diseases (cancer, diabetes, neurodegenerative conditions, infertility, etc.) are associated to the disruption of this balance leading to changes in the activities of both kinases and phosphatases enzymes. Protein phosphatase 1 (PP1) is a major serine/threonine phosphatase, ubiquitous and conserved in eukaryotes. PP1 controls a variety of functions, such as, cell division, transcription, neurotransmission, sperm motility, among others. Protein phosphorylation is one of the ways by which spermatozoa acquire functionality; being PP1γ2 a sperm enriched protein. Moreover, within spermatozoa PP1γ2 is present along the entire length of the tail and equatorial region of the head, suggesting a role in sperm motility and acrossome reaction, respectively. There are several interacting proteins of PP1γ2 which are leading to a revelation of its role in sperm functions. Although there are others, in this thesis, the complex that was the leading point of the study was the new complex SARP2/PP1γ2. This complex includes a new spliced protein firstly described by Browne and co-workers in 2007, which has three different isoforms. In this thesis SARP2 was the isoform used. The complex was found to be enriched in sperm, and this discovery lead to further studies on the possible role of this complex in sperm functions. The relevance of using SARP2 as a putative molecular marker to distinguish normal and abnormal spermatozoa was studied. Since nowadays there is a urgent need to change the way in which men infertility is being diagnosed, especially by the use of the traditional semen parameters evaluated in a spermogram, the biomarker discovery could be a way. In this thesis it was discovered a subcellular localization within human spermatozoa different from the one described before. The expression pattern of SARP2 is very variable; there are fourteen other patterns besides the normal one. Although, it was not possible to confirm with certain that we had a putative molecular marker. The present study gave enough data to proceed in the future, with the elaboration of an optimized experimental plan using more volunteers, to get a representative sample of the Portuguese population. Finally, it is necessary to complement this study with parallel tests (DNA fragmentation, ROS, etc) to ascertain if having a spermatozoon classified as normal, according to our study, is always synonymous of having a normal spermatozoon.
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Liu, Kejun. "Software and Methods for Analyzing Molecular Genetic Marker Data." NCSU, 2003. http://www.lib.ncsu.edu/theses/available/etd-07182003-122001/.
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Genetic analysis of molecular markers has allowed biologists to ask a wide variety of questions. This dissertation explores some aspects of the statistical and computational issues used in the genetic marker data analysis. Chapter 1 gives an introduction to genetic marker data, as well as a brief description to each chapter. Chapter 2 presents the different genetic analyses performed on a large data set and discusses the use of microsatellites to describe the maize germplasm and to improve maize germplasm maintenance. Considerable attention is focused on how the maize germplasm is organized and genetic variation is distributed. A novel maximum likelihood method is developed to estimate the historical contributions for maize inbred lines. Chapter 3 covers a new method for optimal selection of a core set of lines from a large germplasm collection. The simulated annealing algorithm for choosing an optimal k-subset is described and evaluated using the maize germplasm as an example; general constraints are incorporated in the algorithm, and the efficiency of the algorithms is compared to existing methods. Chapter 4 covers a two-stage strategy to partition a chromosomal region into blocks with extensive within-block linkage disequilibrium, and to select the optimal subset of SNPs that essentially captures the haplotype variation within a block. Population simulations suggest that the recursive bisection algorithm for block partitioning is generally reliable for recombination hotspots identification. Maximal entropy theory is applied to choose optimal subset of SNPs. The procedures are evaluated analytically as well as by simulation. The final chapter covers a new software package for genetic marker data analysis. The methods implemented in the package are listed. A brief tutorial is included to illustrate the features of the package. Chapter 5 also describes a new method for estimating population specific F-statistics and an extended algorithm for estimating haplotype frequencies.
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Berry, Simon. "Molecular marker analysis of cultivated sunflower (Helianthus annus L.)." Thesis, University of Reading, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.301959.
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Chani, Eduard. "Molecular marker analysis of a segregating monoploid potato family." Diss., Virginia Tech, 1998. http://hdl.handle.net/10919/29792.
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Anther culture experiments were conducted to construct a monoploid family. The donor plants used were hybrids between high leptine producing selections of Solanum chacoense Bitt. and anther culture responsive selections of Solanum phureja Juz. et Buk. Several steps of the anther culture process were studied. The results indicated that genotype remains the main factor affecting anther culture response. Growing anther-donor plants in higher greenhouse temperatures (30 degrees C day/20 degrees C night) increased the number of embryos per anther by 40 percent. A heat shock given to anthers in culture for 12h at 35 degrees C was also found to be beneficial resulting in an increase of the anther culture response by 40 percent. However the effect of the high temperature shock resulted in lower regeneration rates. In all experiments a highly significant "date" effect was observed with one or two days differing from the others by showing higher response rates in all hybrids tested. The majority of the regenerated plants was diploid, probably resulting from unreduced gametes. Simple sequence repeat analysis with eight polymorphic primer pairs was used successfully to identify the homozygous diploid plants that were added to the monoploids. In total 34 monoploid plants and 14 homozugous diploids were obtained. The degree of heterozygosity revealed by SSR analysis indicated that the diploid plants originated from unreduced gametes formed by first division restitution (FDR) mechanism. The SSR marker data were used to map the genes with respect to the centromeres by half tetrad analysis. SSR-containing sequences from the public databases, as well as sequences obtained from a genomic library enriched for SSRs, were used to generate 48 primer pairs. Only 12 of them were found to be polymorphic in the monoploid family. Ten primer pairs did not amplify any specific fragment. The monoploid population showed distorted segregation at four of the polymorphic loci, showing overrepresentation of the chacoense alleles in three of them. One of the loci showing distorted segregation (STSTP, amplified by primer pair RV 11+12) is most probably linked to lethal alleles, whereas another one (ST13ST, amplified by primer pair RV 21+22) could be linked to genes affecting anther-culture response. The location of the SSR loci on the potato chromosomes is not known except for one (waxy, primer pair 3+4), but statistical analysis on the segregation data obtained from 70 heterozygous anther-derived diploids showed no linkage between them. The SSR primer pairs developed in this study might be useful in studying genetic relationships among cultivars and accessions in breeding programs. Randomly amplified polymorphic DNA (RAPD) analysis was used in association with bulked segregant analysis to detect linkage with genes controlling leptine biosynthesis. With all the limitations imposed by the population size and contamination from foreign pollen, a band amplified by primer OPA-16 could differentiate the bulks contrasting for leptine content. It is possible that this band is linked to genes suppressing leptine biosynthesis, since it appears only in the plants that do not synthesize leptines. Further investigation with larger populations is needed to confirm this possibility.Ph. D.
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Mills, Claire A. "Molecular and non-molecular approaches to creating marker-free transgenic wheat (Triticum aestivum L.) /." [S.l.] : [s.n.], 2000. http://e-collection.ethbib.ethz.ch/show?type=diss&nr=13687.
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Jung, Renata. "Identification of Molecular Markers for Marker-Assisted Selection of Malting Quality and Associated Traits in Barley." Diss., North Dakota State University, 2015. http://hdl.handle.net/10365/25241.
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Barley (Hordeum vulgare L.) is one of the most important cereal crops in North Dakota, which ranks second amongst all states for barley production in the United States. Barley is used for the production of malt, which is used for brewing beer. The malting and brewing industries set strict standards for malt quality; yet, determining malt quality of experimental barley lines is very expensive. For this reason, quality is typically determined at the latter stages of the breeding program, resulting in rejection of many genotypes after large investments for agronomic performance, disease resistance, and end-use quality evaluations have occurred. High quality malt cultivars must possess numerous genetically controlled characteristics. This limits the effectiveness of phenotypic selection for malt quality. The use of marker-assisted selection (MAS) may enable breeders to eliminate lines with undesirable traits earlier in the breeding process, reducing costs, and improving genetic gain. In spite of the large number of mapped QTLs, few examples exist in the literature in which QTL analysis and MAS have been applied to the genetic improvement of malting barley. This research was initiated to identify robust marker-trait associations for malting quality, disease resistance, and agronomic traits utilizing genome-wide association mapping of selected NDSU two-rowed lines. Our research successfully identified numerous marker-trait associations for the traits evaluated to be used for MAS to improve the North Dakota State University barley breeding program.American Malting Barley Association
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Srivastava, Ashok K. "Search for the marker of physiological state in Clostridium acetobutylicum." Thesis, McGill University, 1990. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=74323.
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The potential of selected culture parameters for characterization, quantification and elucidation of the culture physiological state in batch, fed batch and continuous cultivations of C. acetobutylicum was examined in this investigation.The application of theoretical stoichiometric pathway models and on-line NADH fluorescence measurements proved a useful tool in an attempt to assess the intracellular redox state of the solventogenic culture under different growth conditions.
Correlations of key process parameters confirmed the importance of NADH as a regulatory substance in the cell metabolism. A solventogenic culture accumulates more NADH than that in the acidogenic phase. It features an inverse relationship between the specific butanol accumulation rate $(q sb{B})$ and the specific fluorescence (F/X). Fluorescence was also demonstrated to be a suitable control parameter for the regulation of the medium feed rate resulting in constant butanol levels in the fed batch culture.
An improved unstructured mathematical model of the culture system represented the batch acidogenic and continuous culture solventogenic metabolism. However, the culture growth lag occurring in solventogenic transient cultures could only be represented by a structured mathematical culture model which included the markers of "culture growth" (RNA) and "reductive capabilities" (NADH fluorescence) of C. acetobutylicum.
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Mao, Pei-Lin. "Molecular characterization of statin, a protein marker for non-proliferating cells." Thesis, McGill University, 1989. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=59812.
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One cDNA clone (S1) was isolated from a rat brain expression library by statin-specific monoclonal antibodies. S1 contains a statin-like cDNA insert which on amino acid sequence analysis shows a high homology to human elongation factor-1$ alpha$ (EF-1$ alpha$). S1 gene product, pS1, a statin-like protein fused with $ beta$-galactosidase, was cleaved by an endogenous protease from E. coli; therefore, we reconstructed S1 into a pPL-$ lambda$ vector with a thermo-inducible promoter. To verify that this S1 gene product is distinct from the endogenous E. coli EF-Tu, we used the polyclonal antibody HT7, which specifically recognizes the extreme C-terminal of EF-1$ alpha$ also present in S1, but not in the endogenous EF-Tu. The 3$ sp prime$ and 5$ sp prime$ untranslated regions of S1 were found to be completely different from that of EF-1$ alpha$. The level of EF-1$ alpha$ increased during cell proliferation but dramatically decreased in senescent cells. In contrast, S1 mRNA could only be detected in senescent cells. The presence of three different S1-like mRNAs in the rat brain and four in the liver was demonstrated. While both the statin-like S1 gene and EF-1$ alpha$ may belong to the same multigene family, their expression exhibits inverse patterns in proliferating or non-proliferating cells.
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Dockter, Rhyan B. "Genome Snapshot and Molecular Marker Development in Penstemon (Plantaginaceae)." BYU ScholarsArchive, 2011. https://scholarsarchive.byu.edu/etd/2512.
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Penstemon Mitchell (Plantaginaceae) is one of the largest, most diverse plant genera in North America. Their unique diversity, paired with their drought-tolerance and overall hardiness, give Penstemon a vast amount of potential in the landscaping industry—especially in the more arid western United States where they naturally thrive. In order to develop Penstemon lines for more widespread commercial and private landscaping use, we must improve our understanding of the vast genetic diversity of the genus on a molecular level. In this study we utilize genome reduction and barcoding to optimize 454-pyrosequencing in four target species of Penstemon (P. cyananthus, P. davidsonii, P. dissectus and P. fruticosus). Sequencing and assembly produced contigs representing an average of 0.5% of the Penstemon species. From the sequence, SNP information and microsatellite markers were extracted. One hundred and thirty-three interspecific microsatellite markers were discovered, of which 50 met desired primer parameters, and were of high quality with readable bands on 3% Metaphor gels. Of the microsatellite markers, 82% were polymorphic with an average heterozygosity value of 0.51. An average of one SNP in 2,890 bp per species was found within the individual species assemblies and one SNP in 97 bp were found between any two supposed homologous sequences of the four species. An average of 21.5% of the assembled contigs were associated with putative genes involved in cellular components, biological processes, and molecular functions. On average 19.7% of the assembled contigs were identified as repetitive elements of which LTRs, DNA transposons and other unclassified repeats, were discovered. Our study demonstrates the effectiveness of using the GR-RSC technique to selectively reduce the genome size to putative homologous sequence in different species of Penstemon. It has also enabled us the ability to gain greater insights into microsatellite, SNP, putative gene and repetitive element content in the Penstemon genome which provide essential tools for further genetic work including plant breeding and phylogenetics.
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Randhawa, Mandeep Singh. "Molecular Mapping of Rust Resistance in Wheat: Discovery to Deployment." Thesis, The University of Sydney, 2015. http://hdl.handle.net/2123/17216.
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Genetic analysis of seedling stripe rust resistance in a wheat landrace AUS27858 indicated the involvement of two genes. These genes were temporarily named YrAW1 and YrAW2. Single gene segregating F3 families were selected for each gene and recombinant inbred line (RIL) populations were developed. DArT-based bulked segregant analysis located YrAW1 on chromosome 4AL and YrAW2 on 3BS. YrAW1 was formally named Yr51. Markers owm45F3R3 and sun104 flanked Yr51 at genetic distances of 1.2 cM and 2.5 cM on the proximal and distal sides, respectively. Marker sun104 was validated on a set of 40 genetically diverse wheat genotypes. Based on repulsion linkage with Yr4 and absence of any other seedling stripe rust resistance gene in chromosome 3BS, YrAW2 was formally named Yr57. Yr57 was flanked by markers gwm389 and BS00062676 at genetic distances of 2.0 cM and 2.3 cM on the proximal and distal sides, respectively. These markers were validated on set of 23 wheat cultivars.
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Qureshi, Naeela. "Rust Resistance in Wheat: Gene Discovery and Development of Molecular Markers Using Diverse Genomic Resources." Thesis, The University of Sydney, 2017. http://hdl.handle.net/2123/18003.
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This investigation covered characterization of genetically diverse sources of resistance, identification of molecular markers linked with rust resistance genes and their validation across diverse backgrounds. Genetic analysis of leaf rust resistance using durum-specific pathotypes of the leaf rust pathogen revealed the presence of a single gene in Aus26579 and Aus26582. The resistance gene was mapped on chromosome 6BS. Markers sunKASP_60 and sun684 showed close associations with LrAW2. Lr61 was also mapped on chromosome 6BS and haplotype analysis using linked markers suggested that LrAW2 is likely to be Lr61. Aus26582 carried an additional leaf rust resistance gene that was effective against six Australian Pt pathotypes and was mapped on chromosome 3BL and the underlying locus was temporarily named LrAW3. Marker sun786 mapped 1.8 cM distal to LrAW3. As no other seedling leaf rust resistance gene was previously mapped on chromosome 3BL, LrAW3 was formally named Lr79. Markers sun711, sun712, sun725, sunKASP_109 and sun KASP_112 from chromosome 5AL co-segregated with Yr34. Yr48, also located on chromosome 5AL, was proved to be identical to Yr34 on the basis of allelism test, sequence information and haplotype analysis. Various genomic resources were utilized to identify a close genetic association between the marker sun180 and linked rust resistance genes Yr47 and Lr52 in a fine mapping study. The loci order of sun180-0.4 cM-Lr52-0.2 cM-Yr47 was deduced. Markers linked with LrAW2/Lr61 (sunKASP_60), Lr79 (sun786), Yr34/Yr48 (sun712) and linked resistance genes Yr47 and Lr52 (sun180) did not amplify resistance-linked alleles in any of the cultivars lacking these genes and thus demonstrated their robustness in marker-assisted pyramiding with other marker-tagged rust resistance genes to produce triple rust resistant cultivars.
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Cabral, Maria Madalena Ribeiro. "Caspase 3: a potential marker for in vitro fertilization outcome." Master's thesis, Universidade de Aveiro, 2013. http://hdl.handle.net/10773/11733.
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Mestrado em Biologia Molecular e CelularMundialmente é estimado que aproximadamente 70 milhões de casais tenham problemas de infertilidade, o que corresponde a um em cada sete casais em idade reprodutiva. O rápido aumento de problemas reprodutivos nas últimas décadas sugere uma maior probabilidade deste aumento ser devido a factores do estilo de vida e/ou ambientais, do que resultado de uma variação genética. Em Portugal 2,2% dos bébes nascidos resultam de técnicas de reprodução medicamente assistida. A transferência de vários embriões realizada, por vezes, no decurso destas técnicas pode resultar em gravidezes múltiplas, o que advém em complicações bem conhecidas para as mães e os bébes. São necessárias novas ferramentas de diagnóstico para que se possa transferir menos embriões com resultados similares ou melhores. Neste estudo foi investigado o impacto de vários factores do estilo de vida no potencial reprodutivo de 47 casais que recorreram a técnicas de reprodução medicamente assistida. Para além disso, foi realizada também, a correlação entre os níveis de expressão de um marcador da apoptose (caspase-3 clivada) nas células do cumulus do ovócito e a obtenção de uma gravidez (n=30). Uma concentração significativamente (p<0.01)) maior de caspase-3 clivada foi observada nas células do cumulus dos casais que não obtiveram uma gravidez. Dada a dificuldade de obter respostas reais nos questionários dos voluntários e a pequena dimensão da amostra para avaliar parâmetros com tanta variação inter-individual, o estudo não conseguiu obter resultados estatísticamente significativos na correlação do impacto de factores do estilo de vida no potencial reprodutivo. O estudo permitiu concluir que o nível de caspase-3 clivada nas células do cumulus parece ser um bom marcador da qualidade ovocitária e um bom predictor do resultado de gravidez.
Worldwide it is estimated that approximately 70 million couples suffer from infertility, which corresponds to one in each seven couples at fertility age. The rapid increase in reproductive problems in recent decades suggests that they are more likely to be caused by lifestyle and/or environmental factors than as a result of genetic variations. In Portugal 2.2% of the babies born result from an assisted reproduction technology (ART) technique. The multiple embryo transfer performed sometimes in ART techniques may result in multiple pregnancies, which have well known complications for mothers and babies. New diagnostic tools are needed to improve embryo selection, in order to transfer less embryos to achieve similar or better results. In this study the impact of lifestyle factors on the reproductive potential of 47 couples who resort to ART was investigated. Also, the correlation between the expression levels of an apoptotic marker (cleaved caspase-3) in oocytes cumulus cells and the achievement of pregnancy was performed (n=30). Significant (p<0.01) higher concentration of cleaved caspase-3 was observed in cumulus cells of couples who did not achieve pregnancy. Given the difficulty in obtain reliable answers from the volunteers in the questionnaires and the small sample size to evaluate parameters with such a wide inter-subject variability it failed to give conclusive statistical significant data in the lifestyle impact into reproductive potential. The present study allowed concluding that the level of cleaved caspase 3 in cumulus cells appears to be a good marker of oocytes quality and predictor of pregnancy outcome.
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Mendez, Gregory Scott. "Dinoflagellate genomic organization and phylogenetic marker discovery utilizing deep sequencing data." Thesis, University of Maryland, College Park, 2016. http://pqdtopen.proquest.com/#viewpdf?dispub=10159160.
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Dinoflagellates possess large genomes in which most genes are present in many copies. This has made studies of their genomic organization and phylogenetics challenging. Recent advances in sequencing technology have made deep sequencing of dinoflagellate transcriptomes feasible. This dissertation investigates the genomic organization of dinoflagellates to better understand the challenges of assembling dinoflagellate transcriptomic and genomic data from short read sequencing methods, and develops new techniques that utilize deep sequencing data to identify orthologous genes across a diverse set of taxa. To better understand the genomic organization of dinoflagellates, a genomic cosmid clone of the tandemly repeated gene Alchohol Dehydrogenase (AHD) was sequenced and analyzed. The organization of this clone was found to be counter to prevailing hypotheses of genomic organization in dinoflagellates. Further, a new non-canonical splicing motif was described that could greatly improve the automated modeling and annotation of genomic data. A custom phylogenetic marker discovery pipeline, incorporating methods that leverage the statistical power of large data sets was written. A case study on Stramenopiles was undertaken to test the utility in resolving relationships between known groups as well as the phylogenetic affinity of seven unknown taxa. The pipeline generated a set of 373 genes useful as phylogenetic markers that successfully resolved relationships among the major groups of Stramenopiles, and placed all unknown taxa on the tree with strong bootstrap support. This pipeline was then used to discover 668 genes useful as phylogenetic markers in dinoflagellates. Phylogenetic analysis of 58 dinoflagellates, using this set of markers, produced a phylogeny with good support of all branches. The Suessiales were found to be sister to the Peridinales. The Prorocentrales formed a monophyletic group with the Dinophysiales that was sister to the Gonyaulacales. The Gymnodinales was found to be paraphyletic, forming three monophyletic groups. While this pipeline was used to find phylogenetic markers, it will likely also be useful for finding orthologs of interest for other purposes, for the discovery of horizontally transferred genes, and for the separation of sequences in metagenomic data sets.
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Benazir, Katarina Marquez. "Molecular Marker Applications in Oat (Avena Sativa L.) Breeding and Germplasm Diagnostics." Thèse, Université d'Ottawa / University of Ottawa, 2014. http://hdl.handle.net/10393/31148.
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The ability to identify germplasm and select traits accurately is fundamental to successful plant breeding. Pedigrees and molecular markers facilitate these processes; however misleading experimental results can occur when incorrect relationships and/or cultivar names are recorded. Molecular markers can identify these inconsistencies, and with advances in genotyping technology these diagnostics can be done faster and more objectively. This study aimed to develop molecular marker assays and graphical genotyping methodologies for cultivar identification, seed purity assessment and trait selection in oat (Avena sativa L.). KBioscience’s Allele-Specific PCR (KASP™) and genotyping-by-sequencing (GBS) technologies were applied to a set of current Canadian oat cultivars to evaluate their utility for identifying cultivars and detecting intra-cultivar variation. Both KASP™ and GBS detected different extents of heterogeneity among a set of 160 seeds that originated from four seed sources of four cultivars. In both cases, the detected variation did not appear to be limited to a specific cultivar or seed source, reinforcing that all cultivars are heterogeneous. Graphical genotyping localized heterogeneity to specific chromosome regions, thereby distinguishing physical contamination from true genetic heterogeneity and heterozygosity. Pre-existing genotype data for 700 oat cultivars and breeding lines were also used to construct graphical genotypes for pedigree validation and discovery of potential sources for favourable quantitative trait loci (QTL) alleles. This methodology used historical QTLs and anchoring markers to identify 25 putative “high oil” allele carriers. The results from this study will provide diagnostic tools for cultivar identification and pedigree validation, in addition to meaningful information about existing heterogeneity and possible QTL locations in current cultivars.
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Rauwolf, Uwe. "Mapping of genomes and plastomes of subsection Oenothera with molecular marker technologies." Diss., kostenfrei, 2008. http://edoc.ub.uni-muenchen.de/8976/.
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Cartier, Mireille. "Bacterial asparagine synthetase gene as a dominant and amplifiable marker in mammalian cells." Thesis, McGill University, 1990. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=74617.
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The use of the bacterial asnA gene as a dominant and amplifiable marker for a variety of mammalian cells was demonstrated.This gene, coding for asparagine synthetase (AS), was first shown to complement mammalian cells lacking an endogenous AS enzyme. These transfectants proved highly resistant to the glutamine analog albizziin, which inhibits the mammalian AS enzyme. This finding allowed us to use the bacterial AS gene as a dominant marker in wild type mammalian cells, selecting with asparagine-free medium containing albizziin.
Thereafter, amplification of the AS marker in transfectants was achieved through selection of cells in increasing concentrations of the asparagine analog $ beta$-aspartyl hydroxamate (AH).
Studies on the use of the AS marker, alone or in conjunction with other markers, to select for stable, amplified transfectants producing one or more co-transfected gene products are also reported.
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Jensen, Jennifer. "The largest subunit of RNA polymerase II as a molecular marker for inferring land plant phylogeny." Thesis, University of Ottawa (Canada), 2002. http://hdl.handle.net/10393/6333.
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This is an initial study using the gene encoding the largest subunit of RNA polymerase II (RPB1) to elucidate evolutionary relationships among ten land plants. This is the first study to use a single nuclear protein-coding gene to examine seed plant evolution. Results show RPB1 to contain no base compositional bias and to evolve at a conservative rate that is similar in most species studied here. This gene also exists as a single copy in most species and contains enough phylogenetically informative sites to resolve all relationships among the seed plants in this study. Maximum parsimony, neighbor-joining and maximum likelihood analyses all generate identical tree topologies with similar support values at each node. The angiosperms are a monophyletic clade comprised of Nymphaea as the most basal angiosperm, followed by Magnolia, then Arabidopsis and a monophyletic monocot clade containing maize and Oryza . The gymnosperms also form a monophyletic clade with Welwitschia and pine grouped together and sister to a Cycad and Zamia clade. These findings concur with recent studies that refute the Anthophyte theory and place Nymphaea near the root of the angiosperm tree. The RPB1 sequence shows great promise to resolve the phylogenetic relationships among plants.
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Palumbo, Fabio. "Exploiting genomics and molecular markers for plant genetics and breeding." Doctoral thesis, Università degli studi di Padova, 2018. http://hdl.handle.net/11577/3422297.
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Co-dominant molecular markers, such as Microsatellites (or Simple Sequence Repeats, SSRs), are powerful tools for basic and applied research programs in crop plant species. Among the possible applications, they are frequently adopted for genetic traceability of food products, for assessing the genetic diversity of local varieties as well as the genetic identity of modern varieties, and also for marker-assisted breeding purposes. In fact, SSR markers are known to be highly polymorphic and discriminant, well distributed throughout the genome, not affected by environmental factors, more efficient and robust than phenotype-based field trials to detect and predict large numbers of distinct differences/traits among genotypes. However, a review of 90 original articles concerning the varietal characterization of some economically relevant crops in Italy, pointed out a lack of wider consensus among the authors regarding the strategy to design and to adopt for genotyping plant varieties with SSR markers. This study emphasized the urgent need to establish a common procedure concerning: i) the criteria adopted for selecting the marker loci and ii) the genetic parameters to be employed for varietal genotyping.
In order to demonstrate the potentials of these molecular markers, two case studies are presented. A study performed in Agordino, a very old local Venetian landrace of barley (Hordeum vulgare L.), stressed the concrete possibility to use SSR markers for genetic traceability of local varieties and, in particular, of their food derivatives. The genetic characterization of four main corn (Zea mays L.) landraces grown in Veneto (Italy), namely Sponcio, Marano, Biancoperla and Rosso Piave, by means of SSR markers, has shown great utility for monitoring and preventing further genetic erosion, thus preserving their gene pools, phenotypic identities and qualitative traits.
Despite the economic relevance of some crop species, it is common for researchers to deal with the complete lack of SSR data and, more in general, of genomic information. Fennel (Foeniculum vulgare Mill., 2n=2x=22) represents a brilliant example. To overcome this shortage, an Illumina HiSeq 2500 sequencing was carried out in this species, enabling the assembly of the first genome draft in 300,408 scaffolds. The subsequent annotation, permitted to detect and to characterize 103,306 SSR regions. Of these 40 were randomly chosen to design specific primer pairs, preliminary tested and 14 were successfully validated using a core collection of 118 fennel individuals potentially useful for F1 hybrid development. Moreover, the first fennel leaf transcriptome was produced overlapping two transcriptomes, one assembled de novo, the other with an in silico genome-guided approach. A total of 47,775 out of the 79,263 assembled transcripts were annotated and, among them, 11,853 loci contained a putative full-length CDS. Detailed analysis revealed 1,011 transcripts encoding for transcription factors (TFs), 6,411 EST-SSRs, 43,237 SNPs and 3,955 In/Dels. Assembled transcripts were also used to conduct the identification of loci related to the t-anethole biosynthesis, the major component of the fennel essential oils, well-known for its capability in reducing mild spasmodic gastro-intestinal pains as well as for its antithrombotic and hypotensive activity. Finally, detailed analysis revealed 1,011 transcripts encoding for transcription factors (TFs), 6,411 EST-SSRs, 3,955 In/Dels and 43,237 SNPs.
Single nucleotide polymorphisms (SNPs) represent another class of co-dominant markers heavily exploited for the discovery of Mendelian inheritance genes and for the analysis of polygenes or QTLs (quantitative trait loci). Adopting a Genotyping By Sequencing (GBS) approach, the first SNP-based genetic linkage map of leaf chicory (Cichorium intybus L. subsp. intybus var. foliosum, 2n=2x=18) was built using a BC1 population segregating 1:1 for the male sterility (ms) trait. This study enabled the genetic localization of the nuclear ms gene, termed Cims1, within linkage group 9 and the identification of four SNPs that proved to fully co-segregate with the target gene. Considering that this form of male-sterility, controlled by a single recessive nuclear gene, is one of the most effective methods to develop F1 hybrids, our data will be exploitable for marker-assisted selection purposes.I marcatori co-dominanti, tra cui i Microsatelliti (o SSR), sono strumenti molecolari ampiamente utilizzati nell’ambito della ricerca di base e applicata in specie di interesse alimentare. Tra le possibili applicazioni ricordiamo il loro impiego per studi di tracciabilità genetica di prodotti alimentari, per analisi di diversità genetica di varietà locali e identità genetica di varietà moderne e per il miglioramento genetico. Infatti gli SSR sono noti per essere altamente polimorfici e discriminanti, ben distribuiti all’interno del genoma, non influenzati da fattori ambientali, più efficienti e robusti dei marcatori fenotipici nelle analisi di diversità tra genotipi. Tuttavia, un’indagine condotta su 90 articoli scientifici basati sull’identificazione varietale delle specie economicamente più rilevanti in Italia, ha messo in luce la mancanza di un approccio comune tra gli autori in relazione alle strategie da utilizzare per questo tipo di studi. Inoltre lo studio ha evidenziato il bisogno improrogabile di stabilire procedure comuni riguardanti: i) i criteri da adottare per la scelta dei marcatori SSR ii) i parametri genetici più utili a questo scopo. Per dimostrare il potenziale di questa classe di marcatori, vengono presentati due casi studio. Il primo, che ha come oggetto Agordino, un’antica varietà locale veneta di orzo (Hordeum vulgare L.), ha permesso di enfatizzare la possibilità concreta di utilizzare i microsatelliti per la tracciabilità genetica di varietà locali ed, in particolare, di prodotti alimentari derivati. La caratterizzazione delle quattro principali varietà di mais (Zea mays L.) in Veneto -Sponcio, Marano, Biancoperla e Rosso Piave- attraverso marcatori SSR si è dimostrata invece estremamente utile per monitorare e prevenire fenomeni di erosione genetica, consentendo così di preservare la ricchezza genetica che le caratterizza, la loro identità fenotipica e i tratti qualitativi. Nonostante l’interesse economico di alcune specie, non è così raro per i ricercatori doversi interfacciare con la totale mancanza di dati SSR e, più in generale, di informazioni genomiche. Finocchio (Foeniculum vulgare Mill., 2n=2x=22), a tal proposito, rappresenta un esempio calzante. Per sopperire a questa carenza di dati, è stato condotto un sequenziamento su piattaforma Illumina Hiseq 2500, permettendo così l’assemblaggio del prima bozza del genoma di finocchio in 300408 sequenze. La successiva annotazione ha consentito quindi di individuare e caratterizzare 103306 regioni altamente ripetute. Di queste, 40 scelte in modo casuale per il disegno di primer specifici, sono state testate e 14 sono state validate su una popolazione commerciale di 118 individui potenzialmente fruibili per lo sviluppo di ibridi F1. Inoltre, il primo trascrittoma di foglia di finocchio è stato prodotto sovrapponendo due trascrittomi uno assemblato de novo e l’altro in silico, tramite allineamento sul genoma. 47775 dei 79263 trascritti totali sono stati annotati e 11853 risultano contenere una sequenza codificante completa. L’assemblaggio ha quindi consentito l’identificazione di loci coinvolti nella via biosintetica dei trans-anetolo, componente preponderante degli oli essenziali di finocchio e noto per le sue abilità nel ridurre dolori gastro-intestinali nonché per la sua attività antitrombotica e ipotensiva. Analisi dettagliate hanno infine messo in luce 1011 trascritti codificanti per fattori di trascrizione (FT), 6411 microsatelliti (EST-SSR), 3955 inserzioni/delezioni e 43237 polimorfismi a singolo nucleotide (SNP). I marcatori di tipo SNP costituiscono un’altra classe di marcatori codominanti largamente sfruttati per la caratterizzazione di geni ad eredità Mendeliana e per l’analisi di poligeni o loci codificanti tratti quantitativi (QTL). Attraverso un approccio di genotipizzazione tramite sequenziamento (GBS) è stata costruita la prima mappa genetica in radicchio (Cichorium intybus L. subsp. intybus var. foliosum, 2n=2x=18) utilizzando una popolazione BC1 (ottenuta tramite tecniche di reincrocio) segregante 1:1 per il tratto “maschio sterilità”. Questo studio ha permesso di localizzare finemente il gene nucleare della maschio sterilità Cims1 all’interno del gruppo di associazione 9 e ha consentito l’identificazione di 4 SNP co-segreganti a 0 cM con il suddetto gene. Considerato che questa forma di maschio-sterilità, controllata da un singolo allele recessivo nucleare, è uno dei metodi più efficaci per produrre ibridi F1, questi risultati saranno di estrema utilità per studi di miglioramento genetico.
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Cicek, Mine. "Genetic marker analysis of three major carbohydrates in soybean seeds." Diss., Virginia Tech, 2001. http://hdl.handle.net/10919/29300.
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Carbohydrate content sucrose, raffinose, and stachyose are one of the important seed quality traits in soybean. However, little is known about the genetics of these quantitative traits. Recombinant inbred lines (RIL) were developed from the interspecific hybridization between a Glycine max breeding line (V71-370) and a Glycine soja plant introduction (PI407162). The 308 RILs, each parent, and one cultivar were arranged in a randomized complete block design with two replications and planted at two locations in Virginia. The main objective of the first part of this research was to devise a quick, economical, and reliable HPLC methodology to determine the amount of sucrose, raffinose, and stachyose in soybean seeds.
Concentration of sucrose, raffinose and stachyose are quantitative traits, which are hard to manipulate genetically due to the influence of genotype, environment, and genotype by environment interactions on seed chemical composition. The objectives of the second study were to evaluate agronomic and quality traits over locations and to study correlations among traits. The agronomic traits analyzed in this study included; maturity, plant canopy height, canopy spread, leaflet length, leaflet width, yield, and seed size. Seed quality traits studied were sucrose, raffinose, and stachyose content. Although some correlation coefficients were statistically significant at P<0.001, many were not large enough to be of practical value. A positive correlation was observed between all three sugars. Significant variation was observed among RILs and locations for all traits studied. Genotype by environment interaction was significant for all of the agronomic traits, but was not significant for seed sucrose, stachyose, or raffinose. Maturity, seed size, and sucrose content were highly heritable traits, whereas plant height, canopy spread, yield, leaf length, leaf width, stachyose content, and raffinose content had relatively low broad-sense heritabilities.
The RIL population was used to investigate the genetic basis for these agronomic and seed quality traits. Seven out of twenty soybean molecular linkage groups (MLG), A1, A2, E, F, G, I, and M, were selected on the basis of previous research and mapped in this population with restriction fragment length polymorphism (RFLP) and simple sequence repeat (SSR) markers. Five QTL for seed sucrose content, one QTL each for raffinose and stachyose, and one for each agronomic trait except yield and leaflet width, and two QTL each for yield and leaflet width were detected using the Blacksburg data. Four QTL for seed sucrose content, one QTL for raffinose, two QTL for stachyose, one QTL each for plot width and yield and two QTL for leaflet width were detected using the Warsaw data. Several QTL affecting different agronomic traits shared common genomic regions suggesting pleiotropy at some loci. The majority of the seed quality QTL was stable at both locations. Agronomic traits were more environmentally sensitive and no QTL were common to both locations. Epistasis analysis showed interactions between QTL that detected new genomic regions associated with raffinose content. These results suggest that these potential QTL are definitely on the genomic regions of interest and would be more powerful in marker-assisted selection when we find closer markers to each QTL.Ph. D.
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Rattanaprasert, Monchaya. "Construction of a Nisin-Controlled Expression Vector, a Derivative of pMSP3535 for Alternative Selectable Marker." The Ohio State University, 2009. http://rave.ohiolink.edu/etdc/view?acc_num=osu1253160902.
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Jan, Hikmat Ullah. "Efficiency of QTL mapping based on least squares, maximum likelihood, and Bayesian approaches under high marker density." Universidade Federal de Viçosa, 2016. http://www.locus.ufv.br/handle/123456789/7521.
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Conselho Nacional de Desenvolvimento Científico e Tecnológico
Os principais estudos sobre eficiência de mapeamento de locos determinantes de caracteres quantitativos (QTLs) assumiram poucos QTLs de efeito maior, nenhum gene de efeito menor, e reduzida densidade de marcadores moleculares. Este estudo avaliou a eficiência das análises de quadrados mínimos (regressão), de máxima verossimilhança e Bayesiana para o mapeamento de QTLs, assumindo alta densidade de polimorfismos de nucleotídeo único (SNPs), zero a três QTLs e oito ou nove genes de efeitos menores em cada cromossomo, e reduzida proporção da variância fenotípica explicada por cada QTL (reduzida herdabilidade de QTL). Foram também avaliadas a influência do grau de dominância, da herdabilidade, do tamanho amostral, da densidade de marcadores e do efeito de QTL, e as conseqüências do ajuste de modelo aditivo-dominante na ausência de dominância, no mapeamento de QTLs. Foram simuladas 50 amostras de 400 indivíduos F2, os quais foram genotipados em relação a 1000 SNPs (densidade média de um SNP a cada centimorgan) e fenotipados para três caracteres apresentando distintos graus de dominância (dominância unidirecional positiva, dominância bidirecional e ausência de dominância). Para cada característica foi assumido controle por 12 QTLs e 88 genes de efeito menor, distribuídos nas regiões cromossômicas cobertas pelos SNPs (10 cromossomos). As herdabilidade foram 0.3 e 0.7 e os tamanhos amostrais foram 200 e 400. As análises de máxima verossimilhança e de regressão foram equivalentes quanto à eficiência. O mapeamento de QTL não é influenciado pelo grau de dominância, mas é afetado pela herdabilidade, pelo tamanho amostral, pela densidade de marcas e pelo efeito de QTL. A análise Bayesiana apresentou maior poder de detecção de QTLs, maior precisão de mapeamento, e maior número de falso-positivos em comparação às análises de máxima verossimilhança e de regressão. O fator que mais afeta o mapeamento de QTLs é o efeito do QTL.
Previous studies on quantitative trait loci (QTL) mapping efficiency assumed few QTLs of higher effect, no minor genes, and low marker density. This study assessed the efficiency of the least squares, maximum likelihood, and Bayesian approaches for QTL mapping assuming high single nucleotide polymorphism (SNP) density, zero to three QTLs and eight or nine minor genes per chromosome, and low proportion of the phenotypic variance explained by each QTL. We simulated 50 samples of 400 F2 individuals, which were genotyped for 1,000 SNPs (average density of one SNP/centiMorgan) and phenotyped for three traits controlled by 12 QTLs and 88 minor genes. The genes were randomly distributed in the regions covered by the SNPs along 10 chromosomes. The heritabilities were 0.3 and 0.7, and the sample sizes were 200 and 400. The least squares and maximum likelihood approaches were equivalent. The QTL mapping efficiency was not influenced by the degree of dominance but it was affected by heritability, sample size, marker density, and QTL effect. The Bayesian analysis showed greater power of QTL detection, mapping precision, and number of false- positives compared to the least squares and maximum likelihood approaches. The most important factor affecting the QTL mapping efficiency is the QTL effect.
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Havervall, Carolina. "CXCL13: A Prognostic Marker in Multiple Sclerosis." Thesis, Södertörn University College, School of Life Sciences, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:sh:diva-3656.
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In the demyelinating autoimmune disease multiple sclerosis (MS) there is a great need for validated prognostic biomarkers that can give information about both prognosis and disease course. So far only clinical parameters have been shown to predict future outcome. CXCL13 is a potent B cell chemoattractant that has been suggested to be a potential biomarker candidate. The aim of this study was to investigate the usefulness of CXCL13 as a prognostic biomarker for MS.
Clinical, paraclinical, laboratory and MRI data about a large group of MS patients and controls were collected. CXCL13 levels in cerebrospinal fluid (CSF) samples from these patients were determined by standard enzymelinked immunosorbent assay (ELISA).
In general CXCL13 were increased in CSF in MS, especially in relapsing-remitting MS during relapses, i.e. with ongoing inflammations in the central nervous system. CXCL13 is a good candidate prognostic marker for MS, since newly diagnosed MS with high CXCL13 levels showed worsened disease course within five years. Most importantly, MS conversion occurred in higher rate in possible MS patients with high concentrations of CXCL13 in CSF, and in a shorter time point. This observation may support an early treatment decision in these patients.
In conclusion, this study provides support for an association between CXCL13 levels in the CSF and later development of disease severity in MS.
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Mahmoud, Sayed Hassan. "Biochemical marker genes for molecular genetics and plant breeding in Pisum sativum L." Thesis, Durham University, 1985. http://etheses.dur.ac.uk/7853/.
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Three isoenzyme systems (amylase, esterase and glutamate oxalo acetate transaminase) were examined in seeds of pea ( Pisum sativum L.) and showed clear variations in their band patterns on gel electro phoresis between different lines. The inheritance of these isoenzyme systems, and the location of their structural genes on the pea genome were investigated. Reciprocal crosses were made between lines, F2 seeds were analysed for segregation in the band patterns of the isoenzymes, and F2 plants were investigated to find linkage between the genes for these isoenzymes and genes for selected morphological markers. The results obtained showed that each of the investigated isoenzyme systems is genetically controlled by co-dominant alleles at a single locus. The gene for amylase ( Amy ) was found to be on chromosome 2, linked to the loci k and wb ( wb.. .9-k. . .25.. .Amy ). The gene for esterase ( Est ) was found to be linked to the gene Br (chromosome 4) but the exact location is uncertain because of a lack of morphological markers. The gene for glutamate oxaloacetate transaminase ( Got ) was found to be on chromosome 1 linked to the loci a and d ( a...24...Got...41.. d). Gel electrophoresis techniques have also been used to investigate genetically controlled variation in the major subunits (50,000 Mr) of vicilin, a storage protein of Pisum sativum L. The Fl protein band patterns were shown to be additive with respect to those of the parental lines and to be identical in reciprocal crosses. Genetic analysis of the F2 plants indicated that the 50,000 Mr vicilin subunits band pattern is controlled by a pair of co-dominant genes at a single locus. The F2 data were used to locate this major vicilin gene locus ( Vc-1 ) to chromoscane 7, closely linked to the r locus (for round and wrinkled seed surface). A third member of pea legumin gene family, denoted legB, has been sequenced using the "dideoxy chain termination" method with the M1 3 sequencing system. The complete nucleotide sequence showed that this gene has a general form typical of an eukaryotic gene. The homolgies between this gene and the previously published gene "legA" 'were estimated and showed strong homology between the two genes with eight amino acid substitutions and deletion of 14 bp in the third intron (IVS-3).The inheritance of ribosomal RNA (rRNA) genes in ( Pisum sativum L.) was investigated in a cross between two different lines, where length variation in rDNA fragments of Eco RI digests was observed. The results obtained showed that the rRNA genes are controlled by simple Mendelian system with "co-dominance" between alleles. In order to locate the rRNA gene sites to positions on the chromosomes, the segregation of ECO. RI restriction fragments of rDNA from F2 plants with respect to genes for selected morphological markers on chromosomes 4 and 7 (the chromosomes known to have nucleolus organizer regions) were tested. The F2 data showed no linkages between the selected markers and rRNA genes, therefore, in situ hybridization using rDNA radioactive probe ((^3)H- labelled rDNA clone, pHAI) and physical mapping procedures were used. The results obtained have located the rRNA gene sites to nucleolus organizer regions (satellite constrictions) at 138 and 60 map units from the centromeres of chromosomes 4 and 7, respectively.
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Veikondis, Rene. "Genetic characterisation of fungal disease resistance genes in grapevine using molecular marker technology." Thesis, Stellenbosch : Stellenbosch University, 2014. http://hdl.handle.net/10019.1/96090.
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Thesis (MSc)--Stellenbosch University, 2014.ENGLISH ABSTRACT: The aim of this study on grapevine was to genetically characterise, validate and map the reported fungal disease resistance genes of Pölöskei Muskotály (PM), Kishmish Vatkana (KV) and Villard Blanc (VB) in South Africa using QTL analysis. These fungal resistant parents were crossed with other varieties that have desirable fruit qualities in an effort to combine fungal disease resistance with desirable fruit qualities in a single variety. The genetic basis of PM’s resistance to downy and powdery mildew has not been investigated before. It does however have VB in its pedigree so the assumption was made that the same QTL/genes present in VB contribute to this resistance. KV’s resistance to powdery mildew reportedly originates from the REN1 gene located on chromosome 13. VB’s powdery and downy mildew resistance is conferred by QTL present on chromosome 15 and chromosome 18 respectively and has been reported in numerous studies. The study populations comprised of 124 F1 PM x Regal Seedless plants, 16 F1 PM x G4-3418 plants, 14 F1 PM x Sunred Seedless plants, 158 F1 Sunred Seedless x KV plants and 250 F1 VB x G1-6604 plants. DNA was extracted from the leaves and all plants were screened using microsatellite markers. Phenotypic evaluations of downy and/or powdery mildew resistance were performed on the appropriate populations. The molecular data was used to generate linkage maps and combined with phenotypic data to perform QTL analysis. From the molecular data generated for the three PM populations it was determined that the F1 progeny inherited almost exclusively maternal alleles, and could not be used in a mapping study. These populations were eliminated from the study and PM will be used as a pollen donor in future. Molecular data from the Sunred Seedless x KV cross was used to generate a linkage map for chromosome 13 comprising eight markers and spanning 45.6 cM. When combined with the data from two powdery mildew phenotypic screens a QTL peak spanning the REN1 gene on chromosome 13 of KV was identified. This locus explains between 44.8% and 57.7% of the phenotypic variance observed. The molecular data from the VB x G1-6604 cross was used to generate partial linkage maps for chromosome 15 and 18. Eleven markers were mapped on chromosome 15 spanning 56.4 cM, and ten markers were mapped on chromosome 18 spanning 101.8 cM. When the chromosome 15 linkage map was combined with the data from two powdery mildew phenotypic screens a QTL associated with powdery mildew resistance was identified on chromosome 15 that explains between 18.9% and 23.9% of the phenotypic variance observed. Likewise a QTL associated with downy mildew resistance was identified on chromosome 18 when the chromosome 18 linkage map was combined with data from two downy mildew phenotypic screens. This QTL explains between 19.1% and 21.2% of the phenotypic variance observed. This study succeeded in genetically characterising the fungal disease resistance genes of two different sources of grapevine and provided exclusionary information on a third resistance source for future breeding applications.
AFRIKAANSE OPSOMMING: Die doel van hierdie studie in wingerd was om die genetiese komponent van die swamweerstandsgene van Pölöskei Muskotály (PM), Kishmish Vatkana (KV) and Villard Blanc (VB) in Suid-Afrika te karakteriseer en die teenwoordigheid daarvan te bevestig deur ʼn Kwantitatiewe Eienskap Lokus (KEL) benadering te volg. In ʼn poging om swamweerstand en goeie vrugeienskappe te kombineer in ʼn enkel variëteit is die weerstandige variëteite met vatbare variëteite gekruis wat goeie vrugeienskappe besit. Die genetiese basis van PM se weerstand teen donsskimmel en witroes is nog nie vantevore bestudeer nie. VB is een van sy voorgeslagte en daar is aangeneem dat dieselfde KEL/gene waarskynlik verantwoordelik is vir die weerstand. Dit is gerapporteer dat KV se witroesweerstand afkomstig is van die REN1 geen op chromosoom 13. Vele publikasies rapporteer VB se weerstand teen witroes en donsskimmel Beide die witroes- en donsskimmelweerstand word oorgedra deur KEL teenwoordig op chromosome 15 en 18 onderskeidelik. Die populasies gebruik in hierdie studie het bestaan uit 124 F1 PM x Regal Seedless plante, 16 F1 PM x G4-3418 plante, 14 F1 PM x Sunred Seedless, 158 F1 Sunred Seedless x KV plante en 250 F1 VB x G1-6604 plante onderskeidelik. Blare is versamel vir DNS isolasie en genotipering met mikrosatellietmerkers. Al drie populasies se weerstand teen donsskimmel en/of witroes is fenotipies geëvalueer. Die molekulêre data is gebruik om genetiese koppelingskaarte op te stel en gekombineer met die fenotipiese data om KEL analise uit te voer. Die molekulêre data van die drie PM populasies het daarop gedui dat die F1 nageslag amper uitsluitlik moederlike allele geërf het en kon gevolglik nie gebruik word in die studie nie. Die PM populasies is uitgesluit uit hierdie studie en PM sal voortaan as stuifmeelskenker gebruik word. Molekulêre data van die Sunred Seedless x KV kruising is gebruik om ʼn koppelingskaart vir chromosoom 13 op te stel wat 45.6 cM lank is en agt merkers bevat. Die KEL analise van die koppelingskaart en twee fenotipiese datastelle vir witroes het ʼn KEL piek geïdentifiseer wat oor die lengte van die REN1 geen-interval strek. Hierdie lokus is verantwoordelik vir 44.8% tot 57.7% van die fenotipiese variasie wat waargeneem word. Molekulêre data van die VB x G1-6604 kruising is gebruik om gedeeltelike koppelingskaarte vir chromosome 15 en 18 op te stel. Elf merkers karteer op die chromosoom 15 kaart van 56.4 cM en tien merkers karteer op die chromosoom 18 kaart van 101.8 cM. KEL analise van chromosoom 15 se koppelingskaart en twee witroes fenotipiese datastelle het ʼn KEL geïdentifiseer wat 18.9% tot 23.9% van die fenotipiese variasie verduidelik. ʼn KEL is ook op chromosoom 18 geïdentifiseer wat 19.1% tot 21.2% van die fenotipiese variasie verduidelik met die gekombineerde analise van chromosoom 18 se koppelingskaart en twee donsskimmel fenotipiese datastelle. Hierdie studie het die genetiese komponent van die swamweerstandsgene van twee Vitis variëteite suksesvol gekarakteriseer en bevestig. Waardevolle telingsinligting oor die derde variëteit is ook onthul.
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Liu, Sixin. "Molecular marker analysis of adult plant resistance to powdery mildew in common wheat." Diss., Virginia Tech, 1999. http://hdl.handle.net/10919/11236.
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Powdery mildew, caused by Blumeria graminis (DC.) E.O. Speer f. sp. tritici E'm. Marchal (syn. Erysiphe graminis f. sp. tritici), is one of the major diseases of wheat (Triticum aestivum L.) worldwide. The use of cultivars with resistance to powdery mildew is an efficient, economical and environmentally safe way to control powdery mildew. Race-specific resistance has been extensively used in breeding programs; however, it is ephemeral. Adult plant resistance (APR) to powdery mildew is more durable as demonstrated by the cultivar Massey, which has maintained its APR to powdery mildew since its release in 1981. To develop an efficient breeding strategy, it is essential to understand the genetic basis of APR. The objectives of this study were to identify molecular markers associated with APR to powdery mildew in common wheat Massey and to verify their association using recombinant inbred (RI) lines.
A cross was made between the powdery mildew susceptible cultivar Becker and Massey. One hundred and eighty F2:3 lines were rated for disease severity under natural pressure of powdery mildew in field. Using both restriction fragment length polymorphism (RFLP) and microsatellite markers, three quantitative trait loci (QTL), designated as QPm.vt-1B, QPm.vt-2A and QPm.vt-2B, were identified in the Becker x Massey F2:3 generation. These loci are located on chromosomes 1B, 2A and 2B, respectively, and explained 17%, 29% and 11% of the total variation among F2:3 lines for powdery mildew resistance, respectively. Cumulatively, the three QTLs explained 50% of the phenotypic variation among F2:3 lines in a multi-QTL model. The three QTLs associated with APR to powdery mildew were derived from Massey and displayed additive gene action. QPm.vt-2B also fits a recessive model for APR to powdery mildew.
In the second part of this study, 97 RI lines were developed from the Becker x Massey cross. The RI lines were evaluated for APR to powdery mildew under natural disease pressure for three years. Both single marker analysis and interval mapping confirmed the presence of the three QTLs identified in the F2:3 generation. The three QTLs, QPm.vt-1B, QPm.vt-2A and QPm.vt-2B, accounted for 15%, 26% and 15% of the variation of mean powdery mildew severity of the RI lines over three years. In a multi-QTL model, the three QTLs explained 44% of the phenotypic variation of the RI lines. The RI lines were grouped according to the genotype of the three QTLs, represented by markers GWM304a, KSUD22 and PSP3100, respectively. The RI lines with Massey alleles at all three loci had a mean disease severity of 3.4%, whereas the RI lines with Becker alleles at all three loci had a mean disease severity of 22.3%. These severity values are similar to those of the corresponding parents.
The molecular markers identified and verified as to their association with APR to powdery mildew in Massey have the potential for use in marker-assisted selection for resistance to powdery mildew and in pyramiding powdery mildew resistance genes, as well as facilitating a better understanding of the molecular basis of APR to powdery mildew.Ph. D.
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Schrag, Tobias A. "Prediction of hybrid performance in maize using molecular markers." [S.l. : s.n.], 2008. http://nbn-resolving.de/urn:nbn:de:bsz:100-opus-3035.
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Cardona, Cadavid Henry [UNESP]. "Contagem de células somáticas no leite de búfalas e sua aplicação na seleção para resistência à mastite." Universidade Estadual Paulista (UNESP), 2009. http://hdl.handle.net/11449/102792.
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cardonacadavid_h_dr_jabo.pdf: 617128 bytes, checksum: 52904037b788868ea51cbb64af8ea362 (MD5)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)
Na bovinocultura de leite, a alta contagem de células somáticas (CCS) é considerada indicativo da condição de mastite. A mastite ainda continua sendo a doença de maior prevalência em gado leiteiro, causando altos custos. Em rebanhos bufalinos no estado de São Paulo, a presença de mastite subclínica e clínica representam 1,5% e 18,77%, respectivamente, das búfalas em lactação. Isto pode levar à diminuição na produção e na qualidade do leite. Considerando-se que não é possível erradicar essa doença devido a sua origem ser multifatorial (fatores genéticos e ambientais), todos os esforços devem ser concentrados no sentido de manter sua prevalência a mais baixa possível. Assim sendo, o objetivo de nosso estudo foi estimar os parâmetros genéticos para a CCS e produção de leite e identificar polimorfismos nos genes B-defensina 1 e 4. Na estimação dos parâmetros genéticos para a CCS e produção de leite (P305) foram utilizadas 4.907 lactações de 1986 búfalas contidas no arquivo zootécnico mantido pelo Departamento de Zootecnia da Faculdade de Ciências Agrárias da UNESP de Jaboticabal, as quais foram analisadas por meio de inferência bayesiana em análises bicaracterística, empregou-se um modelo animal. Para a caracterização dos genes b-defensina 1 e 4 foram utilizadas amostras de DNA genômico de 132 búfalas de diferentes regiões do estado de São Paulo, empregou-se a técnica de PCR/RFLP (Reação em Cadeia da Polimerase/ Polimorfismo do Comprimento dos xiii Fragmentos de Restrição). As estimativas de herdabilidade da CCSt (h2=0.27) e da P305 (h2=0.25) foram...
In dairy cows, high-somatic cell count (CCS) in milk is considered indicative of the mastitis condition of the mammary gland. Mastitis, inflammation of the mammary glands of dairy animals both clinical and subclinical, results in significant economic losses because of lower milk yields and its degraded quality, early culling and loss of genetic potential, higher veterinary expenses and increased labour costs for a farmer. In buffaloes from São Paulo State, the presence of clinical and subclinical mastitis represent losses between 1,5% and 18,77% of dairy milk buffaloes. This fact causes a diminution of production in the milk quality, interfering in mozzarella production, which is to making utilizing this specie milk. We known that is not possible disappear this illness because their multifactorial source (genetics and environmental factors), all effort will be concentrated in the direction of to keep the prevalence as low that possible. Because the importance of the mastitis in animal dairy, in the last year increase the number of study of defensin genes, which are a group of multifunctional peptides, due to the role played by defensins in defending animals from bacterial, viral, or fungal infections, the genes encoding them seem to be potential markers of the genetically determined susceptibility (or resistance) of the mammary gland. Defensins are present not only in the mammary gland, but also in milk, as well as in leukocyte granules and in macrophages which constitute a part of milk cell population. The β-defensins are cationic peptides. It is a group of antimicrobiana peptides with antibiotic and cytotoxic activity against bacterium xv viruses and fungi. Interest in the β-defensins has grown substantially in recent years, because of their antimicrobiana properties and because... (Complete abstract click electronic access below)
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Lin, Wen-chang. "Histochemical expressing genes as ultrasensitive markers for micrometastasis studies." Case Western Reserve University School of Graduate Studies / OhioLINK, 1992. http://rave.ohiolink.edu/etdc/view?acc_num=case1059657986.
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Sorenson, Laurie. "Molecular Marker Development for the Discrimination of Atlantic and Pacific Blue Marlin (Makaira nigricans)." W&M ScholarWorks, 2011. https://scholarworks.wm.edu/etd/1539617910.
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Aladowicz, E. "RALP, A NOVEL PROGNOSTIC MOLECULAR MARKER IN MELANOMA, IS INVOLVED IN THE NOTCH PATHWAY." Doctoral thesis, Università degli Studi di Milano, 2011. http://hdl.handle.net/2434/155518.
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Melanoma is an aggressive disease with high metastatic potential and resistance to cytotoxic agents. Early-stage melanomas can be successfully cured by surgery and, as in all solid tumours, morbidity and mortality of melanoma are a consequence of local invasion and metastatic spread. The molecular mechanisms involved in the progression of the malignancy, the genetic markers associated to metastatic melanoma dissemination and the acquisition of chemoresistance are only beginning to be defined. An understanding of the molecular biology of melanoma provides a necessary basis to enable the generation of more effective therapeutic modalities.
RaLP, a new member of the SHC family of adaptor proteins was previously characterized in our laboratory as a determinant in the regulation of migration of melanoma cells in short-term assays in vitro. In this study we further characterized the role of RaLP in the progression of melanoma. We have verified that the expression of RaLP significantly correlates with the most important prognostic markers of melanoma (Breslow thickness, Clark’s level of invasion, ulceration, mitotic index and presence of metastasis in lymph nodes) and that patients with RaLP expressing tumours had reduced disease-free survival and overall survival, suggesting that RaLP can be identified as a novel prognostic molecular marker and an independent prediction factor of melanoma progression. We have shown that permanent RaLP silencing does not interfere with the proliferation of three different metastatic melanoma cell lines, while it significantly decreases their migration and this phenomenon was observed even after extended time in culture. The phenotype could be rescued by the overexpression of RaLP in the silenced cells, suggesting that RaLP is a central molecule that positively regulates migration of melanoma cells. Besides regulating migratory abilities of the melanoma cells, RaLP positively influences their invasive potential, by regulating collagen matrix digestion. We also tested cell – cell and cell – ECM adhesion abilities of melanoma cells after RaLP ablation. We observed that RaLP decreases adhesion of the cells to each other in cell – cell adhesion assays and negatively regulates adhesion of melanoma cells to different matrices in cell – ECM adhesion assay. Analyzing gene expression profiles of RaLP – proficient and – deficient cells we have shown that RaLP is involved in the regulation of the NOTCH molecular pathway.
Our in vitro studies suggest that RaLP expression in melanoma might facilitate dissociation of metastatic cells from a tumour mass by loosening cell – cell adhesion, and favour invasion of the surrounding tissues. We still do not know the exact signalling cascade by which RaLP regulates cell motility and adhesion processes and additional studies are necessary to fully understand its role in melanoma progression.
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Ponza, Pattareeya, and pattareeya pon@biotec or th. "Molecular markers of ecotoxicological interest in the rainbowfish Melanotaenia fluviatilis." RMIT University. Applied Science, 2007. http://adt.lib.rmit.edu.au/adt/public/adt-VIT20080102.121231.
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The Crimson-spotted rainbowfish (Melanotaenia fluviatilis) from the Murray-Darling basin of Australia is a common indicator species in Australian ecotoxicology. Biochemical changes have been investigated in this species, but not molecular markers of ecotoxicological interest. In this study genes of M. fluviatilis were isolated using a cDNA library and sequences analysed. Of 345 randomly selected clones, 94 shared similarity with 26 different genes in other organisms in public databases. Amongst these, reproductive genes coding for vitellogenin, retinol binding protein, sialyltransferase and zona pellucida protein were considered of interest in ecotoxicology. The vitellogenin gene was selected for study as it has been widely used as a molecular marker of exposure to 17â-estradiol (E2) in teleosts. Gene expression was examined via northern blot, RT-PCR and Real-Time PCR relative to the housekeeping gene (18S rRNA). The expression of vitellogenin mRNA was observed a t 12 hours post-exposure, peaked at 48 hours according to northern blot analysis; and cleared within 4 days, partly consistent with RT-PCR. However, Real-time PCR yielded an inconclusive result, probably due to differences between pooled and individual samples. Vitellogenin in blood plasma was confirmed by western blot, found to be significantly increased and retained in the plasma in fish treated with E2 compared to controls. It was concluded that vitellogenin mRNA is a molecular marker of exposure to 17â-estradiol in the rainbowfish, and could potentially be used as a marker of exposure to environmental estrogenic chemicals. Further investigations of the expression of genes in the cDNA library, could establish other molecular markers of ecotoxicological interest in M. fluviatilis.
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Utsunomiya, Adam Taiti Harth [UNESP]. "Desenvolvimento e implementação de modelos para simulação de dados SNPs." Universidade Estadual Paulista (UNESP), 2010. http://hdl.handle.net/11449/92613.
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utsunomiya_ath_me_jabo.pdf: 1152493 bytes, checksum: 3f817736ec374e78cf3c1f57eaeab65b (MD5)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)
Um grande volume de informações de marcadores SNPs vem sendo produzidos e aplicados a metodologias de avaliação genética animal. A quantidade de informações disponíveis faz-se um desafio, pois armazená-las e processar-las é demandante computacionalmente. Então, propôs-se com este trabalho 2 algoritmos (MLOCO e MSNP) para simular dados SNPs como alternativa de minimizar a demanda por processamento e consumo de memória computacional. MLOCO simula SNP como um loco que possui configuração de alelos, posição no genoma e efeitos sobre a expressão de fenótipos (nulos para SNP). MSNP simula SNP apenas como loco que possui configuração de alelos e posição no genoma. Ao nível de cromossomo, para MLOCO, poligenes, QTLs e SNPs são armazenados em um único vetor de acordo com suas localizações. Para MSNP, poligenes, QTLs e SNPs também são armazenados de acordo com suas localizações, porém em vetores específicos para cada tipo de loco. Considerando o consumo de memória, MLOCO é menos eficiente porque armazena um número de variáveis maior (efeito do loco, mesmo que seja zero). MSNP não armazena esta variável. Quanto à velocidade de processamento, MLOCO é mais eficiente porque os locos são armazenados de maneira seqüencial, facilitando a amostragem dos alelos devido a variável “posição”, para formação de um gameta e consequentemente um indivíduo. Como o fator limitante na realização de simulações e utilizações de dados é a memória RAM, o MSNP é a melhor alternativa para simular dados SNPs
A large amount of information of SNPs markers have been produced and applied methodologies in genetic evaluation. The amount of information available makes it challenging, for storing and processing them is computationally expansive. So, it was proposed in this paper two algorithms (MLOCO and MSNP) to simulate data SNPs as an alternative to minimize the demand for processing and consumption of computer memory. MLOCO simulates SNP as a locus that has configuration of alleles, position in the genome and its effects on the expression phenotypes (null for SNP). MSNP SNP simulates only locus that has position and configuration of alleles. At the level of the chromosome to MLOCO, polygenes, QTLs and SNPs are stored in a single vector according to their locations. To MSNP, polygenes, QTLs and SNPs are also stored according to their locations, but in specific vectors for each locus type. Whereas the memory consumption, MLOCO is less efficient because stores a greater number of variables (locus effect, even if it is zero). MSNP does not store this variable. As for processing speed, MLOCO is more efficient because the loci are stored sequentially, facilitating the sampling of alleles due to the variable position to form a gamete and hence an individual. As the limiting factor in simulations and use data is the RAM memory, the MSNP is the best alternative for simulating SNPs data
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Grando, Carolina. "Aspectos da demografia do cajueiro-do-campo (Anacardium humile) em áreas de Cerrado do Estado de São Paulo e construção de bibliotecas enriquecidas de microssatélites para a espécie." Universidade de São Paulo, 2009. http://www.teses.usp.br/teses/disponiveis/11/11137/tde-19022010-100235/.
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O cerrado brasileiro é um dos biomas de maior riqueza e endemismo de plantas, mas com alto índice de desmatamento nas últimas décadas, o que resultou na fragmentação dos habtats e na ameaça de extinção de centenas de espécies vegetais. Dentre estas espécies ameaçadas está Anacardium humile, conhecida como cajuzinho-do-campo, uma planta caméfita de ampla distribuição pelo país, servindo de alimento para o homem e para alguns animais e apresentando propriedades medicinais. Estudos sobre a estrutura de populações de Anacardium humile são escassos na literatura, e seu entendimento é fundamental para a preservação e conservação da espécie. Dessa forma, o presente trabalho teve dois objetivos: 1) em duas fitofisionomias de cerrado distintas, estimar a abundância de ramets da espécie, seu padrão de distribuição espacial em macro e microescala, e a influencia da porcentagem de abertura do dossel na determinação deste padrão; 2) a construção de uma biblioteca genômica enriquecida de microssatélites para a espécie e o desenho de primers a partir desta biblioteca, a fim de isolar locos com potencial para uso como marcadores genéticos. Com relação ao primeiro objetivo, três parcelas de 0,5 ha, divididas em 200 subparcelas, foram instaladas (duas num fragmento de cerrado típico à cerradão e uma num fragmento de cerrado aberto), e todos os ramets da espécie foram amostrados por contagem, sendo discriminados os com e sem ataque de Contarinia sp. (Diptera: Cecidomyiidae). Fotografias foram tiradas do centro de cada parcela para determinar a porcentagem de abertura do dossel. A abundância de ramets foi maior nas áreas mais abertas, mas a incidência de ataque de Contarinia sp foi maior no fragmento mais fechado. As análises de macroescala (Índice de Dispersão) e de microescala (Autocorrelação Espacial) mostraram que os ramets da espécie apresentam padrão agregado em ambas as áreas, mas que essa agregação, em microescala, não está relacionada à porcentagem de abertura do dossel, embora haja diferenças significativas para este ultimo fator entre os grids, indicando que o padrão é devido à sua forma de vida. Já em relação ao segundo objetivo, a construção da biblioteca genômica enriquecida de microssatélites resultou em 180 clones, dos quais 84 foram seqüenciados, sendo detectadas 23 sequências contendo microssatélites, o que representa um enriquecimento da biblioteca de 27,38%. Foram desenhados 15 pares de primers dentre os 34 microssatélites obtidos, mas apenas 7 pares amplificaram. Destes, cinco pares foram visualizados em acrilamida, e um loco polimórfico foi observado. O número de clones obtidos está dentro do observado em estudos com outras espécies da família Anacardiaceae, mostrando a eficiência do protocolo. Problemas com a otimização de reagentes podem ter impedido a amplificação de alguns primers, uma vez que os procedimentos para o desenho dos mesmos foram adequados. Os resultados de polimorfismo são preliminares, devido ao número baixo de indivíduos avaliados. Ao menos um loco apresenta potencial como marcador genético.Brazilian cerrado is one of the richest and plants endemism biomes, but with a high deforestation in the last decades, resulted in habitats fragmentation and extinction threat of hundreds of plant species. Among these threatened species is Anacardium humile, known as cajuzinho-do-campo, a camephyth plant with a wide distribution through the country, which serves as aliment to man and some animals and presents some medical properties. Studies about Anacardium humiles populations structure are very scarce in the literature, and its understanding is fundamental to the preservation and conservation of the species. Thus, the present work had two objectives: 1) in two distincts cerrado plant physiognomies, estimate the abundance of species ramets, its spatial distribution pattern in macro and microscale, and the influence of canopy openness percentage in the determination of this pattern; 2) construction of a genomic enriched library with microsatellites to the species and primers design from this library, to isolate loci with potential to be used as genetic markers. In relation to the first objective, three 0,5 ha quadrats, divided in 200 contiguous quadrats of 25 m2, were installed (two in a typical cerrado to cerradão fragment and one in an open cerrado fragment), and all species ramets were sampled by count, being differentiated in with and without Contarinia sp attack ((Diptera: Cecidomyiidae). Photographies of the center of each parcel were taken to determinate the percentage of canopys openness. The abundance of ramets were higher in the most opened areas, but the incidence of Contarinia sp attack were higher in the closest fragment. Macroscale (Dispersion Index) and microscale analysis (Spatial Autocorrelation) showed that species ramets present an aggregated pattern in both areas, but this aggregation is not related to the percentage of canopys openness, although there are significant differences to this last factor among the grids, indicating that pattern is due to its way of life. In relation to the second objective, the construction of genomic library enriched with microsatellites resulted in 180 clones, which 84 were sequenced, being detected 23 sequences containing microsatellites, representing a librarys enrichment of 27,38%. 15 primers pairs were designed among the 34 obtained microsatellites, but only 7 pairs amplified. From these, five pairs were visualized in acrylamide, and one polymorphic loco was observed. The number of obtained clones is in accordance with the observed in studies with another species from Anacardiaceae family, showing protocols efficiency. Problems with the optimization of reagents may have impeded the amplification of some primers, once that procedures to their design were suitable. Polymorphism results are preliminaries, due to low number of evaluated individuals. At least one loco presents potential as genetic marker.
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Laus, Ana Carolina. "Caracterização citogenética molecular de cromossomos marcadores extranumerários." Universidade de São Paulo, 2008. http://www.teses.usp.br/teses/disponiveis/17/17135/tde-06042009-143340/.
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Rearranjos cromossômicos envolvendo a presença de cromossomos marcadores extranumerário são achados citogenéticos freqüentes em pacientes que apresentam deficiência mental, alterações de crescimento, dismorfias e/ou malformações. A presença desse material é responsável por trissomia ou tetrassomia parcial de determinadas regiões cromossômicas, causando quadros clínicos distintos e inespecíficos. A variabilidade fenotípica está relacionada principalmente com os diferentes graus de mosaicismo, os genes presentes na região adicional, o cromossomo de origem, entre outros fatores. Sendo assim, a caracterização desse material cromossômico é de importância fundamental para a determinação do prognóstico e do aconselhamento genético dos pacientes e suas famílias. O presente estudo teve como objetivo a análise de cromossomos marcadores extranumerários por meio de técnicas de citogenética convencional e molecular. Foram selecionados onze pacientes que são acompanhados pelo o Serviço de Genética Médica do Hospital das Clínicas da Faculdade de Medicina de Ribeirão Preto USP, todos com diagnóstico citogenético convencional por bandeamentos GTG de cromossomo marcador extranumerário. Para determinação da origem e caracterização dos cromossomos marcadores foram aplicadas as técnicas de Cariótipo Espectral (SKY) e de Hibridação in situ Fluorescente (FISH). Em dez pacientes foi possível determinar a origem e composição dos marcadores. Dois pacientes apresentam cromossomos marcadores identificados como duplicações invertidas do cromossomo 15, com cariótipos definidos, respectivamente, como 47,XY,+idic(15)(pterq15::q15pter) e 47,XX,+idic(15)(pterq21::q21p11.2), um paciente possui cromossomo marcador derivativo do cromossomo 15, com cariótipo 47,XX,+der(15)(pterq21) e dois pacientes, sendo uma menina e seu pai, possuem cromossomos marcadores derivativos do cromossomo 15 com cariótipos, respectivamente, 48,XX,+2der(15)(pterq12) e 48,XY,+2der(15)(pterq12). Dois pacientes possuem cromossomos marcadores derivativos do cromossomo 9, com cariótipos definidos, respectivamente, como 47,XX,+der(9)(pterq21) e 47,XX,+der(9)(pterq32) e um paciente apresenta cromossomo derivativo do cromossomo 4 [47,XX,+der(4)(p16q21)[9]/48,XX,+der(4)(p16q21),+mar[91]]. Um paciente possui um cromossomo marcador translocado derivativo do cromossomo 22 [47,XY,+der(22)t(11;22)(q25:q11.2)] e outro paciente, um cromossomo translocado derivativo do cromossomo 15 [47,XY,+der(15)t(15;16)(q13;q13)], ambos herdados de mães portadoras de translocações aparente balanceadas. Em um caso, não foi possível a caracterização dos cromossomos marcadores por meio das técnicas aplicadas. Há uma grande variação fenotípica associada à presença de cromossomos marcadores e muitas vezes o prognóstico e o aconselhamento genético são difíceis de determinar. As técnicas de citogenética molecular são ferramentas importantes para a caracterização dos cromossomos marcadores, tanto durante o pré-natal, como para uma família que já possui um membro afetado, auxiliando no mapeamento gênico de cada região envolvida para futura correlação cariótipo-genótipo-fenótipo.Chromosomal rearrangements involving supernumerary marker chromosomes are frequently found in patients with mental retardation, growth defects and malformations. The genetic materials presented in trisomy/tetrasomy are responsible by distinct and unspecific clinical symptoms. The phenotypic variation is related mainly to different mosaicismo degrees, genetic content and chromosomal origin. Thus, the characterization of marker chromosomes is important to determine the prognosis and genetic counseling to the patients and their families. The aim of this study was to analyze supernumerary marker chromosomes using conventional and molecular cytogenetic techniques. Eleven patients were included in this study, all assisted in Medical Genetic Division of Clinical Hospital of School of Medicine of Ribeirao Preto USP. They all presented supernumerary marker chromosomes detected by GTG band. The origin and composition were determined using Spectral Karyotype (SKY) and Fluorescence in situ Hybridization (FISH) techniques. To ten patients, the origin and composition were determined. Two patients presented inverted duplications of chromosome 15, and their karyotype were defined as 47,XY,+idic(15)(pterq15::q15pter) and 47,XX,+idic(15)(pterq21::q21p11.2), one patient had a derivative chromosome 15, with karyotype 47,XX,+der(15)(pterq21), and two patients, a girl and her father, had two derivatives chromosomes 15, with karyotypes 48,XX,+2der(15)(pterq12) e 48,XY,+2der(15)(pterq12), respectively. Two patients presented derivative chromosomes 9 and their karyotype were defined as 47,XX,+der(9)(pterq21) and 47,XX,+der(9)(pterq32), and one patient had a derivative chromosome 4, with karyotype 47,XX,+der(4)(p16q21)[9]/48,XX,+der(4)(p16q21),+mar[91]. One patient had a translocated marker chromosome, derivative 22, [47,XY,+der(22)t(11;22)(q25:q11.2)] and another patient had a translocated marker chromosome, derivative 15 [47,XY,+der(15)t(15;16)(q13;q13)]. In one case, was not possible to define the origin and composition of the marker chromosome using SKY and FISH techniques. A large phenotypic variation is associated with supernumerary marker chromosomes and many times, the prognosis and genetic counseling is difficult to determine. The molecular cytogenetic techniques are important tools to its characterization, during prenatal diagnosis or to a family with an affected person, helping the genetic mapping of each region to a future correlation karyotype-genotype-phenotype.
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Batista, Carlos Eduardo de Araujo. "Diversidade genética molecular em germoplasma de mangueira." Universidade de São Paulo, 2012. http://www.teses.usp.br/teses/disponiveis/11/11137/tde-20022013-151550/.
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A manga (Mangifera indica L.) é uma fruta tropical de origem no continente asiático e umas das principais frutas comercializadas no mundo. A mangicultura apresenta potencial para expandir ainda mais a comercialização de frutos e derivados principalmente, com qualidades para exportação. A produção mundial em média é de 27 milhões de toneladas. Os programas de melhoramento de mangueira necessitam desenvolver cultivares que apresentem o maior número de características agronômicas agregadas. O conhecimento da variabilidade e estrutura genética é almejado pelos melhoristas uma vez que a espécie é perene e apresenta longo o período para obtenção de novas cultivares. Neste trabalho, 151 acessos de mangueira foram analisados quanto a diversidade e estrutura genética do banco de germoplasma. Foram desenvolvidos 23 marcadores microssatélites para caracterização do banco de germplasma de mangueira. Os locos microssatélites apresentaram alto poder informativo para estudos populacionais e observaram-se médias da heterozigosidade esperada de He=0,655, heterozigosidade observada de Ho=0,496 e de PIC = 0,621. Posteriormente a partir dos dados moleculares foram estimados a diversidade e estrutura genética dos 151 acessos e observaram-se 144 alelos com média de 7,2 alelos por loco com amplitude entre 2 e 12 alelos, e uma diversidade gênica média de 0,689. Em todas as simulações estatísticas utilizadas houve consistência em se agrupar os acessos em dois grupos, um grupo formado pelos acessos brasileiros e outro com os acessos norte americanos e os novos híbridos. Uma coleção nuclear foi formada com 30 acessos conseguindo manter 100% dos alelos considerando a diversidade molecular dos 151 acessos de mangueira. Para disponibilizar mais informações ao banco de germoplasma de mangueira da EMBRAPA, 103 acessos contendo informações de 20 locos microssatélites e médias de 48 características agromorfológicas foram avaliadas em conjunto pelo método de otimização de Tocher e formaram-se 23 grupos, onde mais de 50% dos acessos formaram 22 grupos; destes, 10 grupos foram formados por acesso único. Com a finalidade de gerar mais informações para programas de melhoramento da mangueira, um teste de atribuição foi realizado a partir dos dados moleculares e fenotípicos qualitativos, em que também os acessos foram agrupados em dois grandes grupos.The mango (Mangifera indica L.) is a tropical fruit of Asiatic origin and one of the main fruits traded worldwide. The mango crop presents a potencial for further expansion of fruits and derivative trades mainly export qualities. The average world production is 26 million tons. Breeding programs need to develop mango cultivars having the highest aggregate number of agronomic traits. Knowledge of both the genetic variability and structure is aimed by mango culture breeders due to perennial species as well as to the long period of time to obtain new cultivars. In this study, the genetic diversity and structure of the germplasm bank in 151 acessions of mango were analyzed. At first, 23 microsatellite markers were developed in order to extract molecular information from bank germplasm. It was possible to detect that the SSR loci were highly informative in the studied population. Averages were obtained of He = 0.655, Ho = 0.496 and PIC = 0.621. Next, with the molecular data it was possible to estimate the genetic diversity and structure of the 151 acessions as well as observe 144 alleles with an average of 7.2 per locus with amplitude between 2 and 12 alleles; the average gene diversity was 0.689. In all simulations there were consistent statistic analyzes enabling the clustering cultivars in two groups. A group was formed by Brazilian landraces and a second group was formed by North American landraces and Brazilian new hybrids. A core collection of 30 acessions was able to keep 100% of the alleles representing the molecular diversity of 151 mango cultivars. To provide more information to the Embrapa germplasm mango tree, 103 acessions containing information from 20 microsatellite loci and average of 48 agronomic traits were assessed together by the method of Tocher and formed 23 groups. Twenty two groups were formed by more than 50% of acessions while 10 groups were formed by a single acession each. An interactive test was conducted from molecular and qualitative phenotype data which resulted in two consistent clusters.
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Xia, Junnan. "The largest subunit of RNA polymerase II (rpb1) as a phylogenetic marker of seed plant species." Thesis, University of Ottawa (Canada), 2004. http://hdl.handle.net/10393/26812.
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The phylogeny of land plants, especially angiosperms, has been perplexing scientists for more than 125 years. The aim of this study was to help elucidate unanswered phylogenetic issues using rpb1 genes from twenty-six land plant species (8 gymnosperm species, 17 angiosperm species and Psilotum, a fernally, as the outgroup). The sixteen rpb1 genes which were sequenced in this study had very similar lengths and contained no base compositional bias. Synonymous substitutions of rpb1 sequences were saturated when compared to the outgroup. The third codon positions of these genes contained misleading phylogenetic information. The topology of trees based on first and second codon positions were in line with that of protein trees. Both angiosperms and gymnosperms were monophyletic. Amborella was found at the base of the angiosperm tree, followed by Nymphae, then Illicium. These data rejected the anthophyte hypothesis, weakly supported the gnepine hypothesis, but did not resolve the interrelationship among eumagnoliids and eudicots. rpb1 genes were combined with the 18S ribosomal RNA gene and chloroplast atpB and rbcL genes to obtain more robust phylogenies. This combined data set produced a topology similar to that of the first and second positions of rpb1 genes except that they better resolved the interrelationship among eumagnoliids and eudicots. We conclude that our rpb1 sequences evolve too slowly to provide enough phylogenetic information to fully resolve the phylogeny of seed plants and that other gene sequences will need to be added to these data sets to obtain a well-resolved phylogenetic tree of seed plants.
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Olsson, Magnus. "Nuclear pore membrane glycoprotein 210 as a new marker for epithelial cells." Doctoral thesis, Uppsala University, Department of Cell and Molecular Biology, 2003. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-3265.
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Epithelial cell polarisation is a prerequisite for the branching morphogenesis in several organs. Differential screening techniques were used to identify genes, which are upregulated during induction of epithelium in early kidney development. This investigation revealed two separate genes, Nuclear localising protein 1 (Nulp1), a previously undescribed gene with sequence characteristics of the basic helix-loop-helix transcription factor family, and glycoprotein 210 (gp210, POM210), an integral membrane protein constituent of the nuclear pore complex (NPC). Of these, gp210 was found to be upreglated during conversion of mesenchyme to epithelium.
The nuclear envelope, which demarcates the nuclear region in the eukaryotic cell, consists of an inner and an outer membrane that are fused at the locations for NPCs. These large macromolecular assemblages are tube like structures connecting the cytoplasmic and nuclear compartments of the cell. NPCs serve as the only conduits for exchange of molecular information between these cellular rooms. Electron microscopy techniques have revealed detailed information about the NPC architecture. A number of proteins (nucleoporins) have been characterised and embodied as components of the NPC structure. Active, energy dependent nucleocytoplasmic transport of RNAs and proteins is mediated by a group of soluble receptor proteins, collectively termed karyopherins.
Gp210 has been suggested to be important for nuclear pore formation. Nevertheless, our analyses showed a limited expression pattern of gp210, with its mRNA and protein largely confined to epithelial cells in the mouse embryo. Furthermore, in several cell lines, gp210 was undetectable. The expression pattern of gp210 was not synchronised with some other nucleoporins, indicating NPC heterogeneity. Characterisation of the structure of the human gp210 gene, including its promoter region, gave insight about possible cell-type specific gene regulatory mechanisms.
Regulation of molecular traffic between the nucleus and the cytoplasm leads to transcriptional control. Cell specific configuration of the NPC structure, due to diffential expression of gp210, could be involved in this control. Gp210 could be of importance for the development of epithelial cell polarisation.
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Chen, Jianli. "Validation and Marker-Assisted Selection of Two Major Quantitative Trait Loci Conditioning Fusarium Head Blight Resistance in Wheat." Diss., Virginia Tech, 2005. http://hdl.handle.net/10919/25947.
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Fusarium head blight (FHB) is one of the most destructive diseases of common wheat (Triticum eastivum L.) worldwide. Resistance to FHB is an ideal trait for which molecular marker assisted selection (MAS) would facilitate breeding and cultivar development efforts. Validation of quantitative trait loci (QTL) conferring FHB resistance is a prerequisite for MAS. This study was conducted to validate and evaluate the effect of two major QTL, previously reported on chromosomes 3BS and 5AS, on multiple FHB resistance components in two independent studies, one involving a mapping population derived from a cross between a known resistance source W14 and a susceptible soft red winter (SRW) wheat cultivar Pioneer2684, and the other involving seventy adapted SRW wheat lines. The first study confirmed that the 3BS and 5AS QTL were significantly associated with FHB resistance and further indicated that the 3BS QTL has a larger effect on three FHB resistance components (type II and III resistance and resistance to Fusarium Damaged kernels) evaluated in greenhouse experiments, while the 5AS QTL has a larger effect on type I resistance evaluated in a field experiment. Six simple sequence repeat (SSR) and two sequence targeted site (STS) markers associated with FHB resistance in the two QTL regions identified in the first experiment were then used to characterize FHB QTL marker haplotypes and their effect on FHB resistance in seventy wheat genotypes. Five main haplotype groups (1-5) were characterized among the elite lines on the basis of allelic differences of four marker loci linked to the 3BS QTL and two marker loci linked to the 5AS QTL. Haplotype group 5 was comprised of marker allele combinations of both 3BS and 5AS QTL and elite lines with this haplotype have improved type I and type II resistance compared to the other haplotypes. This again validated the presence of QTL on chromosomes 3BS and 5AS, and illustrated the utility of SSR and STS markers in the two QTL regions in selection of FHB resistance in elite backgrounds. Four favorable marker alleles including two (Xbarc133 and XSTS3B142) on 3BS and two (Xbarc117 and Xbarc056) on 5AS are recommended for MAS of the two QTL for improved FHB resistance in wheat. Wheat lines having favorable marker alleles identified in the current study will provide breeding programs with a source of unique and adapted FHB resistant parents and some of the lines also may have potential for release as cultivars.Ph. D.
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Luo, Yuqun. "Incorporation of genetic marker information in estimating model parameters for complex traits with data from large complex pedigrees /." The Ohio State University, 2002. http://rave.ohiolink.edu/etdc/view?acc_num=osu1486549482668451.
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Almeida, Ramon Vinicius de. "Parâmetros genéticos e alterações nas freqüências alélicas em três ciclos de seleção divergente para tolerância ao alumínio em milho." Universidade Federal de Viçosa, 2007. http://locus.ufv.br/handle/123456789/4672.
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Aluminum (Al) toxicity is one of the major constraints for agriculture on acid soils, which occupy large regions of the world s agricultural area. At low pH values associated with these soils Al3+ is solubilized into soil solution and is toxic to plants inhibiting root growth and crop yield. Cultivars genetically adapted to acid soils may offer an environmental compatible solution. The aims of this work were (1) to estimate parameters and genetics gains in three cycles of divergent selection to aluminum tolerance and (2) to identify changes in allelic frequencies at five loci near a QTL in chromosome 5 of maize that explain 13% of the Al tolerance. The phenotypic index employed was relative seminal root length (CLR) obtained from nutrient solution. Simple sequence repeats (SSR) were used to detect linkage disequilibrium between marker and QTL. An expressive genetic gain of 49,15% was observed from base population to first generation. This evidence is characteristic from traits that have oligogenic inheritance. Shifts in allelic frequencies in 4 loci in first generation and in all loci, in second generation were exclusively due to effects of genetic drift.
A toxicidade ao alumínio (Al) é um dos maiores problemas para a agricultura em solos ácidos, que ocupam grandes áreas agricultáveis no mundo. Em condições de baixo pH associado a estes solos, o Al3+ é solubilizado e se torna tóxico para as plantas, inibindo o crescimento de suas raízes e comprometendo a produtividade das culturas. Genótipos adaptados aos solos ácidos podem oferecer uma solução sustentável a este problema. Os objetivos deste trabalho foram (1) estimar parâmetros e ganhos genéticos obtidos ao longo de três ciclos de seleção divergente para a tolerância e (2) identificar alterações nas freqüências alélicas em cinco locos próximos a um QTL no cromossomo 5 do milho que explica 13% da tolerância ao Al. O índice fenotípico empregado, foi o Crescimento Liquido Relativo (CLR) obtido a partir do cultivo em solução nutritiva. Marcadores microssatélites (SSR) foram utilizados para detectar desequilíbrio de ligação entre as marcas e o QTL. Ocorreu um ganho genético expressivo da população base à primeira geração de 49,15%, diminuindo drasticamente para os ciclos posteriores. Tal evidência é patente de caráter de herança oligogênica. Variações nas freqüências alélicas em 4 locos, na primeira geração, e em todos os locos, na segunda geração, foram explicadas exclusivamente pela deriva genética.
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Alazzabi, Mufida. "Insulin-like growth factor-II (IGF2) gene of zebrafish and its use as a biogenetic marker for the assay of epigenetic toxin exposure." Thesis, University of Ottawa (Canada), 2004. http://hdl.handle.net/10393/26561.
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The purpose of this research was to determine whether expression analysis of the IGF2 gene in zebrafish, a gene whose transcription is known to be regulated by DNA methylation in mammals, can be used as a marker or indicator of DNA methylation due to toxin exposure in fish embryos. We examined the expression of IGF2, IGF1, and IGFBP-1 in zebrafish embryos treated with sodium arsenite (thought to inhibit DNA methylation), nickel chloride (thought to cause DNA hypermethylation), trichostatin A (a histone deacetylase inhibitor), 5-azaC (thought to cause methyltransferase inhibition), cadmium chloride (thought to cause DNA hypermethylation) and mercury chloride (unknown). (Abstract shortened by UMI.)
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Amiri, Neda. "Molecular Phylogeny of Poa L. sensu lato (Poaceae) with a Focus on West Asian Species." Thesis, Université d'Ottawa / University of Ottawa, 2016. http://hdl.handle.net/10393/35018.
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Poa L., is known as a highly diverse cosmopolitan genus with taxonomic difficulties that includes unknown species and species with uncertain affinities mainly in West Asia and North Africa. Poa also exhibits a close relationship with two West Asian genera, Eremopoa Roshev. and Oreopoa H. Scholz & Parolly. This study was conducted to: 1) fill the gap of information on the affinities between Poa species with an emphasis on West Asian Poa; 2) revise and evaluate the accuracy of traditional infrageneric classification of West Asian Poa; and 3) clarify the relationship between Poa and two allied genera of Poaceae Barnhart, Eremopoa and Oreopoa. DNA molecular evidence from present phylogenetic analyses of West Asian species of Poa, Eremopoa and Oreopoa, resulted in some great findings as follow: I) Poa caucasica Trin., which is currently assigned to subsection Nivicolae of section Poa from subgenus Poa resolved as a unique new distinct lineage within Poa. II), New treatments are suggested for Poa densa Troitsky, Poa masenderana Freyn & Sint., Poa cenisia All., Poa psychrophila Boiss. & Heldr. and Poa lipskyi. III) Three unclassified species of Poa pseudobulbosa, Poa diversifolia and Poa aitchisonii are assigned here to subgenus Poa and supersection Poa. IV), The present molecular evidence supports inclusion of Eremopoa in Poa and confirms reduction of Eremopoa to a level of subgenus of Poa. V) Present phylogenetic analyses also indicate that monotypic genus Oreopoa H. Scholz & Parolly is part of Poa. These findings require an urgent modification in subgeneric and sectional classification of the genus Poa.
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Peterson, Gregory Warren. "Assessment of two molecular marker techniques in wheat (Triticum aestivum L.) populations segregating for aluminum resistance." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1998. http://www.collectionscanada.ca/obj/s4/f2/dsk2/ftp04/mq28975.pdf.
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Kalantari, Mina. "Human papillomaviruses : role in cervical dysplasia and carcinoma, and use as molecular risk marker for progression /." Stockholm, 1999. http://diss.kib.ki.se/1999/91-628-3631-5/.
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Mazaheri, Lucy. "Development of a Molecular Marker to Track APA G40199 Introgression in Common Bean for Bruchid Resistance." Thesis, North Dakota State University, 2018. https://hdl.handle.net/10365/29300.
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In common bean (Phaseolus vulgaris), the main seed storage pests are the bruchid beetles. Damage done to the seed by the larvae has a large impact on seed quality and yield. Arcelin (ARC), phytohaemagglutinin (PHA), and α-amylase inhibitor (α-AI) are linked seed storage proteins that form the APA locus on chromosome Pv04 and are associated with resistance. A major breeding objective is to introduce bruchid resistance into common bean from a resistant tepary genotype, G40199, by introgressing the resistant APA locus into susceptible common bean backgrounds. Here we developed a molecular marker that tracks the introgression. A set of PCR primers to the α-amylase inhibitor locus amplified a DNA fragment that showed a 45 base pair insertion in the middle of a lectin Leg_b domain. This enhanced locus characterization and insertion/deletion marker may preclude the need for bruchid resistance screening early in the breeding.United States. Agency for International Development
United States. Global Hunger and Food Security Initiative (Cooperative Agreement No. EDH-A-00-07-00005-00)
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Collier, John Michael. "Identification and characterization of p137 a differentially regulated cardiac marker of embryonic trichloroethylene exposure." Diss., The University of Arizona, 1999. http://hdl.handle.net/10150/284051.
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Embryonic trichloroethylene (TCE) exposure was previously shown to be associated with an increased incidence of cardiac birth defects. Although embryo data are lacking exposure studies on adult animals show an association between halogenated hydrocarbon exposure and modifications in gene expression. The present study was undertaken to identify embryonic mRNA transcripts differentially expressed following TCE or metabolite exposure. This study identified numerous differentially regulated transcripts following halogenated hydrocarbon exposure. Examples of upregulated transcripts include stress responsive genes (Hsp 70, Hsp 70 cognate), a Ca²⁺-ATPase, calreticulin and serum response factor while downregulated transcripts include Midkine (RARP), numerous ribosomal proteins (8s, 18s, 24s), p137 and vimentin. p137 was a candidate sequence marked for further study to determine whether this sequence could be utilized as a molecular marker of TCE exposure. p137 showed a correlation between increased levels of maternal TCE exposure and decreased levels of transcript expressed in E11 fetal tissue. Immunohistochemical staining using an affinity purified antibody to p137 demonstrates widespread expression in rat E11 and chicken St. 17 embryos. p137 protein is broadly expressed in chicken St. 13 through St. 22 heart, but by St. 29 becomes more restricted in the ventricular myocardium with continued endocardial expression. At stages between St. 13 and St. 17 in chick embryos the ectodermal epithelium, yolk sac epithelium, dermatome, developing optic vesicle and neural tube express p137 protein. To explore potential function of p137, atrioventricular explants were exposed to affinity purified p137 antibody. Results show that p137 antibody treatment blocks epithelial-mesenchymal transformation of endothelial cells in-vitro. This study shows that p137 is expressed during rat and chicken mid-gestation in heart and other epithelial tissue derivatives and appears to play a role in the epithelial-mesenchymal transformation of the cardiac atrioventricular cushions. p137 is identified as a useful marker of developmental exposure to halogenated hydrocarbons and its altered expression may contribute to the phenotype of the affected heart.