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1

Varrieur, John Michael. "AFLP Marker Analysis Of Monoploid Potato." Thesis, Virginia Tech, 2002. http://hdl.handle.net/10919/33177.

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Potato haploids have been recent components in protoplast fusion research, strategies to combine wild and cultivated potato germplasm and the generation of economically valuable mutant phenotypes. Additionally, most major genetic mapping and QTL analyses in potato have utilized haploid germplasm to simplify linkage-mapping computations. The accuracy of genetic assumptions concerning the randomness and genetic purity of haploid genomes may directly affect the statistical validity of many results in current potato research. In the present study, AFLP analysis was conducted on two sibling S. phureja "BARD 1-3" monoploid populations derived by androgenesis in anther culture, and gynogenesis through the use of a haploid-inducing pollinator, S. phureja "IVP 101." Little indication of somaclonal variation and haploid-inducer gene introgression was found in the monoploid band data suggesting genomic stability. Segregation of marker alleles that were heterozygous in the parent was distorted from the expected 1:1 ratio in both populations, ranging from 35% in the gynogenic monoploids (GM) to 46% in the androgenic monoploids (AM). Genetic diversity appeared more random among the monoploid populations after skewed marker data was removed from phylogenetic analyses. Bilateral and unilateral marker skewness in the monoploid populations may respectively indicate common and unique segregation distorting loci (SDL) present in the AM and GM genomes. Representatives of both SDL types were located on a partial linkage map created using androgenic monoploid data.
Master of Science
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2

Al, Kaabi Helel Humaid Saed Humaid. "Date palm tissue culture and AFLP analysis of plant variability." Thesis, Imperial College London, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.409314.

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3

Dasmahapatra, Kanchon Kumar. "The use of AFLP markers for estimating relatedness and inbreeding." Thesis, University of Cambridge, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.614696.

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4

Badenhorst, Daleen. "Development of AFLP markers for Haliotis midae for linkage mapping." Thesis, Stellenbosch : Stellenbosch University, 2008. http://hdl.handle.net/10019.1/21525.

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Thesis (MSc)--Stellenbosch University, 2008.
ENGLISH ABSTRACT: Haliotis midae, is the only commercially important species of the six abalone species found in South African coastal waters and has become a lucrative commercial commodity. Wild stocks of H. midae are, however, no longer commercially sustainable due to a combination of environmental factors and poaching. The solution to the crisis is artificial production systems in the form of abalone farms. An abalone enhancement programme was initiated in South Africa in 2006, funded by industry and government. This programme focuses on the elucidation of the abalone genome and genetic factors contributing to increased productivity, thereby aiding the commercial production of abalone. The aims of this study, the first of its kind concerning H. midae, were to develop AFLPbased markers (specifically fluorescent AFLP analysis); to monitor the segregation of these markers in a single full-sib family and to use the markers and additional microsatellite markers to generate the first preliminary linkage map for H. midae. Genomic DNA of sufficient quality and purity for fluorescent AFLP analysis was obtained from 3.5-month-old H. midae juveniles. Preliminary linkage maps were constructed using AFLP and microsatellite markers segregating in an F1 family following a pseudo-testcross mapping strategy. Twelve AFLP primer combinations, producing 573 segregating peaks, and 10 microsatellite markers were genotyped in the parents and 108 progeny of the mapping family. Of the 573 segregating AFLP peaks genotyped, 241 segregated in a 1:1 ratio and 332 in a 3:1 ratio. Of these AFLP markers, 90 segregated according to the expected 1:1 Mendelian ratio and 164 segregated according to the expected 3:1 Mendelian ratio at the P = 0.05 level and were used for linkage analysis. Of the 10 microsatellite markers genotyped, nine were informative for linkage mapping analysis. Preliminary male and female genetic linkage maps were developed using markers segregating in the female or male parent. A total of 12 and 10 linkage groups were detected for the female and male maps respectively. The female map covered 1473.5cM and consisted of 56 markers, and the male map covered 738.9cM consisting of 30 markers. Markers with segregation distortion were observed as previously reported in other abalone species and potential homology between one of the linkage groups of the male map and two of the linkage groups of the female map were identified using the 3:1 segregating AFLP markers. In conclusion, the genetic linkage map presented here, despite the fact that it has relatively low genome coverage and low marker density, forms an ideal starting point for more detailed study of the H. midae genome and will provide a scaffold for basic and applied studies in abalone. A high-density linkage map of H. midae should in future be developed with additional co-dominant molecular markers, such as microsatellites, to improve the transferability of the linkage map between different laboratories and among populations. A high-density linkage map will facilitate the mapping of QTL of commercially important traits (i.e. growth) and future MAS breeding programmes.
AFRIKAANSE OPSOMMING: Perlemoenspesie, Haliotis midae, is die enigste spesie van kommersiële belang van die ses wat in die kuswater van Suid-Afrika aangetref word en het ‘n winsgewende handelskommoditeit in Suid-Afrika geword. Die ontginning van natuurlike H. midae populasies is egter, as gevolg van ‘n kombinasie van omgewingsfaktore en stropery nie meer kommersieel volhoubaar nie. Die perlemoenkrisis kan die hoof gebied word deur kunsmatige produksiesisteme op perlemoenplase tot stand te bring. ‘n Perlemoen verbeteringsprogram is in 2006 in Suid-Afrika geïnisieer en word deur die industrie en regering befonds. Die program focus op die ontrafeling van die perlemoen genoom en die genetiese faktore wat bydrae tot verhoogde produksie. Sodanige inligting kan gebruik word om kommersiële perlemoenproduksie te bevorder. Die doel van hierdie studie, die eerste met H. midae, is om AFLP-gebaseerde merkers (spesifiek fluoresserende AFLP analise) te ontwikkel; die segregasie van hierdie merkers te monitor in ‘n enkel volledige verwante familie en die merkers en addisionele mikrosatelliet merkers te gebruik om die eerste voorlopige koppelingskaart vir H. midae te genereer. Genomiese DNS van genoegsame kwaliteit en suiwerheid vir fluoresserende AFLP analise is ge-ekstraeer uit 3.5-maand-oue H. midae individue. Voorlopige koppelingskaart is gekonstrueer deur van segregerende AFLP en mikrosatelliet merkers in ‘n F1 familie gebruik te maak deur ‘n pseudo-kruistoets karteringstrategie te volg. Twaalf AFLP inleier kombinasies, wat 573 segregerende fragmente geproduseer het, en 10 mikrosatelliet merkers is gegenotipeer in die ouers en 108 individue van die nageslag van die karteringsfamilie. Van die 573 segregerende AFLP merkers wat gegenotipeer is, het 241 in ‘n 1:1 verhouding en 332 in ‘n 3:1 verhouding gesegregeer. Van hierdie AFLP merkers, het 90 volgens die verwagte 1:1 Mendeliese verhouding en 164 volgens die 3:1 Mendeliese verhouding by die P = 0.05 gesegregeer vlak en is vir die koppelingsanalise gebruik. Van die 10 mikrosatelliet merkers gegenotipeer, was 9 informatief vir koppeling karteringsanalise. Voorlopige manlike en vroulike genetiese koppelingskaarte is ontwikkel met gebruik te maak van merkers wat in die manlike of vroulike ouer segregeer het. ‘n Totaal van 12 en 10 koppelingsgroepe is onderskeidelik in die vroulike en manlike karate gegenereer. Die vroulike kaart dek 1473.5cM and bestaan uit 56 merkers, terwyl die manlike kaart 738.9cM beslaan het met 30 merkers. Merkers wat segregasie distorsie toon is waargeneem soos voorheen in ander perlemoenspesies gerapporteer. Potensiële ooreenstemming tussen een van die koppelingsgroepe van die manlike kaart en twee van die koppelingsgroepe van die vroulike kaart is aangetoon deur van die 3:1 segregerende AFLP merkers gebruik te maak. Die genetiese koppelingskaarte verskaf wel ‘n relatiewe lae genoomdekking en ‘n lae merkerdigtheid, maar is ‘n ideale vertrekpunt vir meer gedetailleerde studie van die H. midae genoom en dien as ‘n raamwerk vir toekomstige basiese en toegepaste studies in perlemoennavorsing. ‘n Hoëdigtheid koppelingskaart van H. midae moet in die toekoms ontwikkel word met gebruik van bykomstige ko-dominante molekulêre merkers, soos mikrosatelliete. Dit sal die oordraagbaarheid van die koppelingskaart tussen verskillende laboratoria asook tussen populasies verbeter. ‘n Hoëdigtheid koppelingskaart sal die kartering van kwantitatiewe kenmerk loki (KKL) vir kommersieel belangrike kenmerke (onder andere groeikrag) en toekomstige merker bemiddelde seleksie (MBS) teelprogramme moontlik maak.
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Reck, Maikel. "Estudos moleculares em Hypochaeris catharinensis Cabrera (Asteraceae) utilizando marcadores AFLP." UEL. IAPAR. EMBRAPA. Centro de Ciências Biológicas. Programa de Pós-Graduação em Genética e Biologia Molecular, 2010. http://www.bibliotecadigital.uel.br/document/?code=vtls000159604.

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Hypochaeris catharinensis, pertencente ao gênero Hypochaeris (Asteraceae), é uma espécie endêmica do sul do Brasil. A fim de determinar a estrutura genética de populações desta espécie e a sua posição filogenética dentro do grupo sul-americano do gênero, foram utilizados marcadores moleculares AFLP (Amplified Fragment Length Polymorphism). Para definir a posição filogenética de H. catharinensis dentro do grupo sul-americano de Hypochaeris, foram aplicados onze primers seletivos de AFLP em oito diferentes espécies sulamericnas de Hypochaeris (H. megapotamica, H. pampasica, H. neopinatifida, H. argentina, H. apargioides, H. lutea, H. petiolaris e H. variegata) além da espécie testada H. catharinensis e de H. angustifolia, considerada como o possível ancestral do grupo sulamericano de espécies, que foi usada como outgroup. Os resultados AFLP de mostraram a formação de três dos grupos filogenéticos já definidos previamente. Hypochaeris catharinensis associou-se fortemente (booststrap de 90%) com H. lutea, dando origem a um novo grupo filogenético entre as espécies sul-americanas de Hypochaeris. Este grupo encontra suporte nas caracterísitcas cariotipicas, compartilhadas por H. catharinensis e H. lutea. Assim, foi proposto neste trabalho a formação de um novo grupo filogenético (grupo Lutea) composto por essas duas espécies. Para o estudo de populações, seis combinações de primers de AFLP foram aplicadas em 11 populações de H. catharinensis coletadas no sul do Brasil renderam 183 fragmentos sendo 90,16% polimórficos. As análises obtidas para os dados de AFLP mostraram que a porcentagem de variabilidade genética é maior dentro (83,64%) do que entre (16,36%) as populações de H. catharinensis. A análise da coordenada principal mostra que a maioria das 11 populações estudadas apresentam indivíduos misturados entre as populações, revelando a ausência de um claro padrão de isolamento. Fatores como tempo de divergência recente juntamente com as características endêmicas e morfológicas, que favorecem a dispersão a longa distância, podem ter contribuído para o pouco grau de diferenciação encontrado.
Hypochaeris catharinensis (Asteraceae) is endemic to south Brazil. In this work we used AFLP molecular marks (Amplified Fragment Length polymorphism) aiming to determine the genetic structure of H. catharinensis and to define its phylogenetic position within the South American group of the genus Hypochaeris. To define the phylogenetic position of H. catharinensis, eleven AFLP selective primer combinations were used in eigth diferent South American Hypochaeris plus H. catharinensis and H. angustifolia, used as outgroup. The results showed three main phylogenetic groups, as defined in previous studies. Hypochaeris catharinensis formed a tight association (90% booststrap) with H. lutea, giving origem to a new phylogenetic group, named Lutea group. This group is also supported by the similarities observed on the karyotypes of H. catharinensis and H. lutea. Together these data provide valuable information that may help to elucidate the processes of adaptative radiation of the genus Hypochaeris into the South American continent. Six AFLP primes combinations, applied in 11 populations of H. catharinensis coleted from the Santa Catarina and Rio Grande do Sul states, rendered 183 frangents of which 165 (90,16%) were polymorphic. AMOVA, applied to the AFLP data revealed that the genetic variability was higher within (83,64%) than among (16,36%) populations. Principal Coordinate Analysis showed that most of the 11 populations studied have individuals that are mixed in other populations, revealing the absence of a clear pattern in the genetic structure. The recent divergence of the South American Hypochaeris, together with the morphological and ecological characterists that favour the seed dispersion of H. catharinensis, may have contributed to the low level of divergence observed among populations of this species.
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6

Callak, Kirisozu Asude. "Molecular Characterization Of Blumeria Graminis F. Sp. Hordei Using Aflp Markers." Master's thesis, METU, 2009. http://etd.lib.metu.edu.tr/upload/3/12611153/index.pdf.

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Blumeria graiminis f. sp. hordei (powdery mildew) is an obligate biotroph infecting hordeum vulgare (barley). It is one of the most devastating pathogens of barley, decreasing barley yield in great extent. In order to decrease barley loss, numerous studies are being conducted for overcoming the disease from the sides of both pathogen and host. However the pathogen is evolving very rapidly preventing the effective use of pesticides such as fungisides or development of resistant barley varieties by crossing race-specific resistance varieties, varieties having R genes, with susceptible but high yield producing varieties. In order to understand the mechanism of pathogen-host interactions, and producing enduring solutions for the problem of yield loss in barley molecular tools need to be used. In this thesis study, Amplified Fragment Length Polymorphism (AFLP) molecular marker method is used in order to reveal the molecular characterization of Turkish Blumeria graminis f. sp. hordei varieties collected from Ç
ukurova region in Turkey. Thirty-nine samples were analyzed with eigth universal races, of which virulence genes are studied. AFLP studies were conducted on LI-COR 4300 DNA Analyzer system. Bioinformatics analysis was performed with NTSYS program. By the help of this Numerical Taxonomic System, similarity, dissimilarity, clustering, dendograms, two-dimensional scatter plots, and three-dimensional perspective plots were obtained. By the light of these analyses Turkish Blumeria graminis f. sp. hordei varieties together with universal races are grouped into three clusteres. In conclusion, studying Turkish Blumeria graminis f. sp. hordei isolates and comparing them with universal races is a unique study in terms of characterizing the Turkish Bgh isolates for the first time, and can be used as a frontier study for studying Resistance genes, by reverse genetic tools.
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7

Potter, Tara. "AFLP markers linked to Fusarium head blight resistance in Triticum aestivum." Thesis, University of Ottawa (Canada), 2002. http://hdl.handle.net/10393/6321.

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In this study, AFLP technology was used to find markers linked to genes controlling Fusarium head blight (FHB) resistance in Triticum aestivum L. FHB is a disease of cereal crops that results in reduced wheat yields, discoloured, shrivelled kernels, mycotoxin accumulation, and reduced seed and grain quality. Since resistance mechanisms in wheat are complex, often being confounded by environmental effects, and there is high genotypic variance for resistance, molecular markers closely linked to FHB resistance would help in the screening of resistant germplasm. Candidate markers for resistance that were found among three varieties of wheat, two being susceptible to FHB ('Karena' and 'AC Cartier') and one being resistant to FHB (FHB 148), were followed into double haploid (DH) F2 from crosses between each of the susceptible varieties and the resistant variety. These DH lines were evaluated for resistance after inoculation with F. graminearum and MAXR linear regression was done to determine whether any of the candidate markers could explain the variation in phenotype. In the 'Karena'/FHB 148 DH lines, 67% of the polymorphisms segregated in a 1:1 Mendelian fashion (p ≥ 0.05), while 50% segregated 1:1 in the 'AC Cartier'/FHB 148 DH lines (p ≥ 0.05). In the 'Karena'/FHB 148 population, 35% of the variation in the FHB resistance phenotype was explained by two markers (p ≤ 0.05), while in the 'AC Cartier'/FHB 148 population, two markers explained 29% of the variation in phenotype (p ≤ 0.05). Cloning and sequencing of these markers would be useful in the development of cultivars resistant to FHB by marker assisted selection.
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Rojas, Thaís Cabrera Galvão. "Utilização de AFLP para estudos genéticos em Prochilodus argenteus (Pisces, Prochilodontidae)." Universidade Federal de São Carlos, 2008. https://repositorio.ufscar.br/handle/ufscar/5448.

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Universidade Federal de Sao Carlos
Genetic studies have been performed for an endemic species from São Francisco River basin, Prochilodus argenteus, which has a great importance in the artisanal and subsistence fishing in the region. The linkage mapping and the genetic variability studies were made with AFLP (Amplified Fragment Length Polymorphism) dominants markers and with 189 specimens from a F1 cross, that was also used for restocking the upstream area from Três Marias hydroelectric dam. All the analyses were carried out with 15 primer pairs combinations and the linkage map was made using the pseudo-testcross mapping strategy. Forty six heterozygous marks were found for the genitors, with mendelian segregation of 1:1. The female genitor map had 3 linkage groups and the lenght of the analysed genome was 128,45 cM, the male genitor map had the same number of linkage groups and the total length of 192,67 cM. Common markers for both genitors, with mendelian segregation ratio of 3:1, served as bridge between the maps, for the construction of an integrated map. This map had 9 linkage groups, and the total map length was 442,08 cM. Additionally, the genetic variability was assessed and an expected heterozygosity mean was of 0,32082, with a Jaccard s similarity coefficient of 0,72564 + 0,00451. These preliminary values show that the cultured sample has a higher similarity coefficient than that obtained for the wild populations. Hence, the present results suggest that genetic studies and management restocking practices should be simultaneously performed for the maintenance of the genetic patrimony of this species at the São Francisco River basin. The results also showed that AFLP marks were suitable and effective to identify linkage marks in Prochilodus argenteus and for genetic variability studies in cultivar samples.
Estudos genéticos foram realizados em uma espécie endêmica da bacia do rio São Francisco, Prochilodus argenteus, a qual possui grande importância na pesca artesanal e de subsistência da região. Os estudos do mapa de ligação e de variabilidade genética foram realizados com o uso do marcador dominante AFLP (Polimorfismo de Comprimento de Fragmentos Amplificados) e com 189 indivíduos de um cruzamento F1, utilizado também para o repovoamento do rio São Francisco, à montante da barragem de Três Marias (MG). Todas as análises foram realizadas com 15 combinações de primers. Para a construção dos mapas de ligação foi utilizada a abordagem pseudocruzamento teste. Os primers utilizados geraram 46 marcas heterozigóticas para os genitores, com segregação mendeliana de 1:1. O mapa referente ao genitor feminino apresentou 3 grupos de ligação e o comprimento do genoma analisado foi de 128,45 cM, e o mapa do genitor masculino também consistiu em 3 grupos de ligação com comprimento total de 192,67 cM. Marcadores comuns aos dois genitores, com segregação mendeliana de 3:1, foram utilizados como pontes na integração dos mapas. O mapa integrado foi formado por 9 grupos de ligação, o que correspondeu a 442,08 cM de genoma analisado. Adicionalmente, a variabilidade genética foi estudada por meio da média da heterozigosidade esperada (He), a qual foi de 0,32082 e pela análise do coeficiente de similaridade de Jaccard, que foi igual a 0,72564 + 0,00451. Estes valores, ainda que preliminares, mostraram que essa amostragem cultivada possui o coeficiente de similaridade maior quando comparado com os de populações selvagens. Desta forma, sugere-se no presente trabalho que estudos genéticos devam ser realizados juntamente com a prática de repovoamento de rios, visando conservar o patrimônio genético desta espécie na bacia do São Francisco. Os resultados mostraram também que os marcadores AFLP foram adequados e eficientes para a identificação de marcas ligadas em Prochilodus argenteus e no estudo da variabilidade genética de amostras cultivadas.
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Purvis, Andrew Ian. "AFLP markers for the study of somatic recombination in Phytophthora infestans." Thesis, Bangor University, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.322560.

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10

Chang, Yeun-Kyung. "Amplified fragment length polymorphism (AFLP) analysis of genetic variability in Phalaenopsis." Thesis, Virginia Tech, 2008. http://hdl.handle.net/10919/34361.

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Amplified fragment length polymorphism (AFLP) markers allow a rapid assessment of the level of genetic variation that would be difficult to evaluate using a limited number of morphological markers. AFLP was used to assess the level of genetic variation among 16 different Phalaenopsis species and hybrids. Ten AFLP primer combinations were used for genetic analysis of these Phalaenopsis and 95% of polymorphism in 16 Phalaenopsis species and hybrids was detected. The genetic similarity among Phalaenopsis species and hybrids ranged from 0.298 to 0.774 based on Dice coefficient. The dendrogram derived by UPGMA analysis clustered into two main groups. A significant linear relationship (r2 = 0.524, P < 0.0001) was observed between known pedigrees and AFLP-derived genetic similarity for 136 pairwise comparisons of Phalaenopsis species and hybrids. The results indicate that there is an abundance of genetic diversity among within Phalaenopsis and that AFLP can be used to distinguish morphologically similar genotypes.

In a second study, the effect of gametophytic selection on genetic diversity in Phalaenopsis was examined by AFLP analysis. Sixteen F1 seedlings resulting from cross-pollination that occurred within high (30 ºC) and low (14ºC) temperature incubators between two hybrid Phalaenopsis [P. (Taisoco Windian à Sogo Yukidian) by P. hybrid unknown], were subjected to genetic analysis by AFLP. A total of 651 fragments ranging in size from 100 to 350 bp were detected using six primer combinations, of which 387 (59.4%) were polymorphic. Seedlings derived from different temperature treatments exhibited 25.5% to 35.9% polymorphism. The genetic similarity among 16 F1 seedlings ranged from 0.825 to 0.946 based on the Dice coefficient. A dendrogram based on 387 polymorphic markers was derived by UPGMA analysis resulting in three major groups and one subgroup. The dendrogram analysis showed clear clustering in Phalaenopsis hybrids pollinated under different temperature treatments, suggesting that several loci may have been selected during the divergent temperature stress treatments during pollination and early pollen tube growth.
Master of Science

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Suzaki, Vitor Junji. "Filogenia e biogeografia do complexo Croton pallidulus(Euphorbiaceae), inferidas por sequências de DNA e marcadores AFLP." Universidade de São Paulo, 2011. http://www.teses.usp.br/teses/disponiveis/41/41132/tde-23042012-140006/.

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O projeto abordou a detecção de polimorfismos genéticos num Complexo formado por algumas espécies de ampla ocorrência no Sudeste-Sul do Brasil, cuja delimitação ainda não está muito bem estabelecida, por apresentar grande polimorfismo morfológico que suscita dúvidas quanto a se tratar de uma única ou de várias espécies. Foram estudadas as seguintes espécies: C. ceanothifolius, C. dichrous, C. erythroxyloides, C. aff. erythroxyloides, C. myrianthus, C. pallidulus var. pallidulus, C. pallidulus var. glabrus e C. splendidus. A proposta do presente trabalho foi avaliar a consistência das espécies estudadas, por meio de análise filogenética baseada em sequências de ITS e duas regiões do DNA do cloroplasto (trnL-F e rps16), e por meio de marcadores AFLP (Amplified Fragment Length Polymorphism). Como grupo externo foi utilizado C. urucurana. Como objetivo adicional procurou-se estudar filogeograficamente as espécies do Complexo, por meio de análises de populações disjuntas, distribuídas desde o Sudeste até o Sul do país. Inferências filogenéticas foram realizadas a partir das seqüências de DNA, realizadas através dos critérios de máxima parcimônia e probabilidades posteriores (análise bayesiana). Os resultados foram uma grande união da maioria das espécies do Complexo em uma politomia; as populações de C. Dichrous e C. aff. Erythroxyloides surgiu separadamente em um clado, assim como duas populações de C. Pallidulus var. glabrus com C. Myrianthus, além de três populações de C. Pallidulus var. pallidulus e outras espécies do Complexo emergirem em outro clado. Pela técnica de AFLP, obtiveram-se fragmentos polimórficos, utilizados como caracteres nas relações de afinidade genética através da análise Neighbor-Joining (realizada no programa PAUP). Observou-se que as duas variedades de C. pallidulus emergem em clados diferentes, enquanto as duas populações de C. pallidulus var. glabrus emergem em um mesmo clado. C. pallidulus var. pallidulus apresentou-se como táxon parafilético, na medida em que aparece agrupada com diferentes espécies, resultado este que confirma a natureza distinta destas duas variedades. C. erythroxyloides e C. aff. erythroxyloides mostraram, através dos dois métodos de análises moleculares, ser espécies distintas. C. splendidus, C. ceanothifolius e C. myrianthus não estão bem resolvidas, misturando-se, muitas vezes com C. pallidulus var. pallidulus. Por fim, foi verificada a congruência entre as topologias obtidas com a análise baseada na combinação dos dados de sequenciamento com aquela obtida por AFLP. O estudo de biogeografia indicou que a área de distribuição ancestral do grupo provavelmente é ampla, localizando-se entre Minas Gerais e Santa Catarina, uma vez que a distribuição das espécies do complexo se dá preferencialmente nestes estados
The project addressed the detection of genetic polymorphisms in a Complex formed by some species of widespread occurrence in southeast of Brazil, whose limits are not yet well established, by presenting great morphological polymorphism that raises doubts as to whether it is a single or various species. The following species were studied: C. ceanothifolius, C. dichrous, C. erythroxyloides, C. aff. erythroxyloides, C. myrianthus, C. pallidulus var. pallidulus, C. pallidulus var. glabrus and C. splendidus. The purpose of this study was to evaluate the consistency of the species studied by means of phylogenetic analysis based on sequences of ITS and two chloroplast DNA regions (trnL-F and rps16), and by AFLP markers (Amplified Fragment Length Polymorphism). Was used as outgroup C. urucurana. As additional objectives, we tried to study the phylogeography of the species complex, through analysis of disjunct populations distributed from the Southeast to the South. Phylogenetic inferences were made from DNA sequences, performed by the criteria of maximum parsimony and posterior probabilities (Bayesian analysis). The results were a great union of most species of the Complex in a polytomy; the populations of C. dichrous and C. aff. erythroxyloides emerged separately in a clade, apart from two populations of C. pallidulus var. glabrus with C. myrianthus, besides the three populations of C. pallidulus var. pallidulus and other species of Complex emerging in another clade. For the AFLP technique, we obtained polymorphic fragments used as characters in the genetic affinity relationships through the neighbor-joining analysis (performed using the PAUP). It was observed that the two varieties of C. pallidulus emerge in different clades, while the two populations of C. pallidulus var. glabrus emerge in the same clade, C. pallidulus var. pallidulus appeared as a paraphyletic taxon, as it appears grouped with different species, a result that confirms the distinct nature of these two varieties. C. erythroxyloides and C. aff. erythroxyloides shown by the two methods of molecular analysis, to be distinct species. C. splendidus, C. ceanothifolius and C. myrianthus are not well resolved, blending, often with C. pallidulus var. pallidulus. Finally, there was congruence between the topologies obtained with the analysis based on combined sequencing data with that obtained by AFLP. The study of biogeography indicated that the distribution area of the ancestral group is probably wide, situated between Minas Gerais and Santa Catarina, since the distribution of species of the complex occurs preferentially in those states
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12

Costa, Bárbara Letícia Pereira. "Caracterização fenotípica e genotípica de isolados de Actinobacillus pleuropneumoniae provenientes de diferentes estados brasileiros." Universidade de São Paulo, 2017. http://www.teses.usp.br/teses/disponiveis/10/10134/tde-27072017-151034/.

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A infecção por Actinobacillus pleuropneumoniae, doença conhecida como pleuropneumonia suína, assumiu grande importância na suinocultura moderna devido à alta ocorrência observada nos rebanhos. O impacto da doença está relacionado à capacidade do agente em causar pneumonia severa, levando os animais a óbito ou doença crônica, resultando em graves prejuízos zootécnicos. Diante desse cenário, o controle e monitoramento do agente se faz importante por meio da identificação dos diferentes sorotipos, da análise genética e da determinação dos perfis de resistência aos antimicrobianos. O objetivo do presente estudo foi caracterizar fenotípica e genotípicamente estirpes de Actinobacillus pleuropneumoniae isoladas a partir de quadros de pneumonia em suínos. Um total de 85 estipes de A. pleuropneumoniae foram submetidas a reação em cadeia pela polimerase (PCR) para identificação e sorotipagem, determinação da concentração inibitória mínima de antimicrobianos, polimorfismo do comprimento de fragmentos amplificados (AFLP) e eletroforese em gel de campo pulsado (PFGE). Os sorotipos mais frequentes foram: 5 (38,8%), 10 (29,4%), 7 (5,9%), 8 (5,9%) e 6 (3,5%), sendo que 14 (16,5%) estirpes foram não tipáveis. Foi observada alta heterogeneidade de perfil genético entre as estirpes analisadas, tanto pelo AFLP quanto pelo PFGE, e o índice discriminatório para cada técnica foi 0,97 e 0,84, respectivamente. Todas as estirpes foram sensíveis ao ceftiofur, gentamicina, tulatromicina e tilmicosina, sendo que 98,8% das estirpes foram resistentes à tilosina e altas taxas de resistência foram observadas ainda para as tetraciclinas, clindamicina e sulfadimetoxina.
Infection by Actinobacillus pleuropneumoniae, a disease known as swine pleuropneumonia, has gained greater relevance to modern pig farming due to the high recurrence rate observed in herds. The impact of the disease relates to the capacity of the agent to cause severe pneumonia, leading to animal death or chronic conditions, thus resulting in severe zootechnical losses. In view thereof, the control and monitoring of the agent is key, being performed through the identification of different serotypes, genetic analysis and determination of antimicrobial resistance profiles. The objective of this study was to characterize phenotypically and genotypically Actinobacillus pleuropneumoniae strains isolated from swine with clinical presentation of pneumonia. A total of 85 strains of A. pleuropneumoniae were subject to polymerase chain reaction (PCR) for identification and serotyping, determination of the minimal inhibitory concentration, amplified fragment length polymorphism (AFLP) and pulsed field gel electrophoresis typing techniques (PFGE). Most recurring serotypes were: 5 (38.8%), 10 (29.4%), 7 (5.9%), 8 (5.9%) and 6 (3.5%), of which 14 (16.5%) strains were nontypeable. High genetic heterogeneity was observed for both AFLP and PFGE, and the discriminatory index for each technique was 0.97 and 0.84, respectively. All 85 strains were susceptible to ceftiofur, gentamicin, tulatromicin and tilmicosin, 84 of which were resistant to tylosin, and high resistance rates were also observed for clindamycin, tetracyclines and sulfadimethoxine.
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13

Castilla, Karina Salvagni. "Caracterização genotípica de cepas de Haemophilus parasuis." Universidade de São Paulo, 2008. http://www.teses.usp.br/teses/disponiveis/10/10134/tde-23012009-164010/.

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Haemophilus parasuis é um dos agentes bacterianos que tem assumido grande importância na indústria suinícola nos últimos anos. Por muitos anos foi considerada uma doença esporádica de suínos jovens, no entanto, com o surgimento de doenças imunossupressoras ou com o aumento da criação de suínos com alto status sanitário, sua freqüência vem assumindo proporções cada vez maiores. A caracterização das cepas através de métodos fenotípicos como a sorotipagem não tem sido suficiente para os estudos epidemiológicos sobre esta bactéria, uma vez que muitos isolados não são sorotipificáveis. Os objetivos deste estudo foram caracterizar os isolados através da sorotipagem, do Polimorfismo do Comprimento de Fragmentos Amplificados (AFLP) e da Eletroforese em Gel de Campo Pulsado (PFGE), comparando os resultados obtidos. Dentre as 51 cepas de Haemophilus parasuis avaliadas uma foi classificada como sorotipo 2, doze como sorotipo 4, seis como sorotipo 5, quatro como 13 e sete como sorotipo 14, sendo que vinte e uma amostras não foram sorotipificáveis. Através do AFLP foi possível caracterizar todos os isolados, com um índice discriminatório de 0,98, porém esta técnica não demonstrou uma boa reprodutibilidade. Através da PFGE utilizando a enzima Sma I apenas 14 cepas foram genotipadas, porém com a enzima Not I, todas apresentaram padrões de bandas e o índice discriminatório obtido foi de 0,95. Os perfis obtidos através da PFGE com a enzima Not I apresentaram a melhor correlação com os dados de origem das cepas e seus sorotipos, indicando que a técnica possui um bom potencial para aplicação em estudos epidemiológicos.
In recent years, Haemophilus parasuis has had a growing impact on the swine industry. In the past, Haemophilus parasuis infections were considered to be sporadic in young pigs. However, the incidence is increasing due to immunosuppressive diseases and the increase in the production of pigs with high sanitary status. Characterization of strains using methods based on phenotype identification is not enough to perform epidemiological studies on thebacterium, since a large percentage of isolates are nontypeable). The aim of this study was to characterize isolates according to serotyping, Amplified Fragment Length Polymorphism (AFLP), and Pulsed Field Gel Electrophoresis (PFGE), and to compare characterization results. Out of the 51 strains of Haemophilus parasuis evaluated in this study: one was serotype 2; twelve serotype 4; six serotype 5; four serotype 13; and seven serotype 14. Serotyping could not be performed on the remaining 21 samples. All isolates were characterized using AFLP, with a discriminatory index of 0.98, but reproducibility of this technique is not good. Regarding PFGE, 14 strains were genotyped using enzyme Sma I; yet, with enzyme Not I, all strains presented band size and discriminatory index power of 0.95. The profiles obtained using PFGE with Not I presented better correlation with the origin and serotype of the strains, suggesting that this technique could be used in epidemiological studies with promising results.
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Bajay, Miklos Maximiliano. "Diversidade e estrutura genética de Piptadenia gonoacantha (Mart.) J.F. Macbr. em áreas em processo de restauração florestal e remanescentes de Mata Atlântica." Universidade de São Paulo, 2014. http://www.teses.usp.br/teses/disponiveis/11/11137/tde-02062014-132710/.

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A Mata Atlântica é considerada mundialmente um dos biomas prioritários para conservação, devido à elevada riqueza de sua biodiversidade. A preservação da vegetação natural deve estar associada à restauração florestal, de modo que se possa assegurar a continuidade desta rica biota. No Brasil, grande parte dos projetos de restauração florestal realizados até agora tem se preocupado apenas em buscar diversidade florística, contemplando uma baixa diversidade genética em sua implantação, o que têm criado muitos problemas relativos à viabilidade biológica de suas comunidades. O presente trabalho se propôs a realizar um estudo comparando a diversidade genética (utilizando marcadores SSR, cpSSR e AFLP) da espécie arbórea Piptadenia gonoacantha (Mart.) J. F. Macbr. em duas áreas em processo de restauração florestal e dois remanescentes naturais de floresta estacional semidecidual da Mata Atlântica do estado de São Paulo, Brasil. A partir da biblioteca genômica construída, foram obtidos 12 locos SSR. A heterozigosidade média esperada no equilíbrio de Hardy Weinberg (HE = 0,494) foi maior do que a heterozigosidade observada (HO = 0,251) em todas as populações, indicando taxa relativamente alta de endogamia (FIS = 0,342). Os resultados obtidos com os locos cpSSR mostraram, ao todo, 16 haplótipos, dos quais 10 foram encontrados nos remanescentes de floresta nativa e oito nas áreas restauradas. As análises realizadas com os marcadores AFLP resultaram em 303 marcas polimórficas. Uma estrutura genética muito forte foi encontrada relativa às quatro populações, valores de FST foram 0,283, 0,83 e 0,177 em SSR, cpSSR e AFLP, respectivamente. Dez locos de AFLP que podem estar sujeitos a seleção foram encontrados. As análises de agrupamento delimitam claramente as amostras das quarto populações, evidenciando que não existe fluxo gênico significativo entre elas. P. gonoacantha apresentou auto correlação espacial nas quatro populações. Os três tipos de marcadores detectaram maior diversidade genética nos remanescentes naturais do que nas áreas restauradas. Apesar da menor diversidade apresentada pelas áreas restauradas em comparação com as áreas de remanescentes florestais, o tamanho efetivo populacional estimado para essas áreas permite a manutenção da variabilidade existente a curto prazo. As informações obtidas poderão servir para o manejo sustentado desta espécie, bem como para o planejamento de sua conservação.
The Atlantic Forest is considered one of the world biomes for conservation priority due to the high richness of its biodiversity. The preservation of natural vegetation should be associated to forest restoration, so that the continuity of this rich biota can be ensured. Recent studies and practices of reforestation in degraded areas have taken population genetics as a great ally. Several of the forest restoration projects carried out in Brazil so far has been concerned just with floristic diversity, contemplating low genetic diversity. This fact has created many problems related to the biological viability of their communities. The present project proposes to carry out a study on the diversity genetic structure of the arboreal species Piptadenia gonoacantha (Mart.) J. F. Macbr. In this study, we used six chloroplast simple-sequence repeats (cpSSRs), AFLP markers and the construction of an enriched SSR DNA library to investigate the genetic diversity of P. gonoacantha. This species was evaluated in two areas that are under forest restoration process and compared then with two natural remnants of semideciduous seasonal Atlantic Forest. 12 SSR markers were obtained and the average HO=0.251 was smaller than the average HE=0.494, evidencing a heterozygote deficit (average FIS= 0.342). The samples shows a strong structure with a significant differentiation. FST values were 0.283, 0.83 and 0.177 for SSR, cpSSR and AFLP respectively. The cluster analyzes clearly demarcating the samples of the four populations. cpSSR markers showed 16 haplotypes, ten of them were found in the remaining native forest and eight in the restored areas. Ten AFLP outliers loci were found. The three types of markers detected a higher genetic diversity in natural remnant than in restored areas. Despite the lower diversity presented by the restored areas compared with areas of forest remaining, the effective population size estimated for these areas allows the maintenance of existing variability. The results of this study prove that there is greater genetic diversity in the remaining natural areas than in the areas undergoing a reforestation process. The information obtained may be used for the sustainable management of this species, as well as for conservation planning.
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Gomes, Cleise Ribeiro. "Isolamento e caracterização genotípica de cepas de Bordetella avium através da eletroforese em campo pulsado (PFGE) e polimorfismo do comprimento de fragmentos amplificados (AFLP)." Universidade de São Paulo, 2011. http://www.teses.usp.br/teses/disponiveis/10/10134/tde-25092012-110758/.

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A Bordetella avium é o agente etiológico da bordetelose aviária, uma doença altamente contagiosa que afeta o trato respiratório superior das aves. B. avium adere-se preferencialmente às células do epitélio ciliado traqueal, promovendo inflamação e deformação da mucosa respiratória. As infecções do trato respiratório das aves resultam em grandes prejuízos para toda indústria avícola, desta forma, o presente estudo teve como objetivo a caracterização genotípica e de sensibilidade a antimicrobianos de isolados de B. avium provenientes de perus com histórico de aerossaculite. Dentre os 300 animais examinados, isolou-se B. avium de 13 aves e foram selecionadas 20 cepas do agente para os estudos posteriores. Através do antibiograma realizado pela técnica de disco difusão observou-se um alto número de cepas resistentes aos antimicrobianos beta lactâmicos (amoxacilina, ampicilina, penicilina e ceftiofur), assim como para lincomicina, sulfonamidas e combinação sulfonamidas/trimetoprima (cotrimoxazol) e uma grande heterogeneidade resultando em 15 perfis distintos. Os antimicrobianos com maiores níveis de sensibilidade foram o florfenicol, seguidos pelas quinolonas, doxiciclina e pelas tetraciclinas. Todas as cepas foram caracterizadas através da PFGE e do AFLP, apresentando 15 pulsotipos e 16 perfis genotípicos respectivamente. Os métodos fenotípicos e genotípicos apresentaram capacidade discriminatória semelhante e revelaram uma grande diversidade dentre os isolados analisados.
Bordetella avium is the etiologic agent of avian bordetellosis, a highly contagious disease that affects the upper respiratory tract of birds. B. avium adheres preferentially to ciliated tracheal epithelial cells, promoting inflammation and deformation of the respiratory mucosa. Infections of the respiratory tract of birds resulting in large losses for the entire poultry industry in this way, this study aimed to characterize genotypic and antimicrobial susceptibility of isolates of B. avium from turkeys with a history of Airsacculitis. Among the 300 animals examined, B. avium was isolated from 13 turkeys and 20 strains were selected for further studies. Through the antibiogram performed by disk diffusion technique was observed a high number of strains resistant to beta-lactamic antibiotics (amoxicillin, ampicillin, penicillin and ceftiofur), as well as, lincomycin, sulfonamides and sulfonamide combination/ trimethoprim (cotrimoxazole) and a high level of heterogeneity resulting in 15 different profiles. The antimicrobials with higher levels of sensitivity were florfenicol, followed by quinolones, doxycycline and tetracycline. All strains were characterized through to PFGE and AFLP, presenting 15 pulsotypes and 16 genetic profiles, respectively. Phenotypic and genotypic methods showed similar discriminatory capacity and presented a high diversity among isolates examined.
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16

Zucon, Luciane Tieko Shinya. "Caracterização fenotípica e genotípica de amostras de Salmonella spp. isoladas de suínos." Universidade de São Paulo, 2008. http://www.teses.usp.br/teses/disponiveis/10/10134/tde-16072008-151833/.

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Entre os microrganismos relevantes para a segurança alimentar, bactérias do gênero Salmonella tem se destacado como causadoras de toxinfecções, sendo motivo de preocupação constante para a cadeia de produção de aves e suínos. Os objetivos deste trabalho foram estudar a ocorrência de Salmonella spp. em suínos sadios ao abate e em animais apresentando sinais clínicos de salmonelose, tipificação dos isolados através da sorotipagem, polimorfismo do comprimento de fragmentos amplificados (AFLP) e eletroforese em gel de campo pulsado (PFGE). Foram examinados 50 animais com sintomatologia sugestiva de salmonelose de 12 granjas dos Estados de São Paulo, Paraná e Rio Grande do Sul e analisadas amostras de fezes, linfonodos e suabes de carcaças de 124 animais de quatro frigoríficos do Estado de São Paulo. Dos suínos com sintomatologia clínica, 38% dos animais foram positivos para o isolamento de Salmonella spp., sendo selecionadas 45 cepas, classificadas como S.Typhimurium (29/45), S. Choleraesuis (9/45), S. Infantis (3/45) e S. enterica subsp. enterica (4/45). Dos 124 suínos sadios, 16,12% foram positivos para o agente, sendo isoladas 39 cepas que foram classificadas como S. London (11/39), S. Anatum (11/39), S. Typhimurium (8/39), S. Agona (2/39), S. Enteritidis (2/39) e S. enterica subsp. enterica (5/39). Através do AFLP, a caracterização genética dos isolados revelou índice discriminatório igual a 0,85 e gerou 12 perfis distintos. O índice discriminatório do PFGE foi 0,96 apresentando 31 padrões distintos. Ambas as técnicas possibilitaram uma boa correlação entre isolados, seus sorotipos e locais de isolamento, sugerindo grande potencial para sua aplicação na genotipagem de Salmonella spp.
Among relevant microorganisms to food security, Salmonella has been highlighted as a major cause of food borne diseases, being a constant concern for poultry and pig production chain. The goal of this study was to investigate the Salmonella spp incidence in healthy pigs at slaughter, as well as in pigs showing salmonellosis clinical signs, characterize strains by serotyping, Amplified fragment length polymorphism (AFLP) and Pulsed field gel electrophoresis (PFGE). Fifty animals, presenting salmonelosis suggestive clinical symptoms, from 12 swine herds from Sao Paulo, Parana and Rio Grande do Sul states were examined and clinical materials such as stool samples, lymph nodes and carcass swab from 124 animals from four Slaughterhouses in Sao Paulo state were analyzed. Among the pigs with clinical symptoms, 38% of the animals were positive for the Salmonella spp. isolation. Forty five strains were selected and classified as S.Typhimurium (29/45), S. Choleraesuis (9/45), S. Infantis (3/45) and S. enterica subsp. enterica (4/45). From the 124 healthy pigs studied, 16.12% were positive for the agent. Thirty nine strains were isolated and classified, by serotyping, as S. London (11/39), S. Anatum (11/39), S. Typhimurium (8/39), S. Agona (2/39), S. Enteritidis (2/39) and S. enterica subsp. enterica (5/39). Through AFLP, genetic characterization of isolates showed discriminatory index of 0.85 and generated 12 distinct profiles. The PFGE discriminatory index was 0.96, showing 31 distinct patterns. Both techniques allowed a good correlation between the isolates, its serotypes and isolation locations, suggesting great potential of its application in genotyping of Salmonella spp.
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17

Mistak, Daniel Joseph. "AFLP markers demonstrate male heterogamety in a fathead minnow (Pimephales promelas) population." Online access for everyone, 2008. http://www.dissertations.wsu.edu/Thesis/Spring2008/d_mistak_042208.pdf.

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18

Konzen, Enéas Ricardo. "Análise morfológica, bioquímica e genética do brilho do tegumento em variedades de feijoeiro (Phaseolus vulgaris L.)." Universidade de São Paulo, 2011. http://www.teses.usp.br/teses/disponiveis/64/64133/tde-09022012-103001/.

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Diversas características interferem na aceitabilidade de variedades de feijoeiro (Phaseolus vulgaris L.) no mercado consumidor, como o brilho do tegumento. Geralmente, o feijão com brilho é rejeitado para consumo, pois apresenta difícil cozimento. No entanto, o brilho pode conferir resistência ao ataque de insetos e patógenos à semente, podendo constituir uma vantagem para o melhoramento do feijão. A presença de brilho é devida à expressão do gene Asp (Asper) na forma alélica dominante. Genótipos aspasp, portanto, apresentam tegumento opaco. Outro gene, J (Joker), interfere na expressão da característica, de modo que o alelo recessivo j diminui a intensidade do brilho e altera a coloração do tegumento. J é considerado o precursor de polifenois denominados pró-antocianidinas. Na presença j estes compostos não são sintetizados. No presente trabalho foram genotipadas variedades de feijoeiro crioulas [Serro Azul Brilhante (SAB - tegumento brilhante) e Fosco (SAF - tegumento opaco) e Puebla-152 (P-152 - brilhante)] e a cultivar Diamante Negro (DN - opaco), contrastantes para o brilho do tegumento. Análises fenotípicas, morfológicas e bioquímicas permitiram inferir os genótipos das variedades e avaliar a segregação do brilho em populações derivadas de cruzamentos entre contrastantes: SAF x SAB e P-152 x DN. Os resultados mostraram que as variedades não variam para J, apenas para Asp, sendo que SAB e P-152 carregam Asp e SAF e DN o alelo asp. Em todos os cruzamentos a segregação foi de três brilhantes (Asp) para um opaco (asp) na geração F2 e de cinco brilhantes para três opacos em F3. A partir dos resultados, as variedades foram contrastadas por meio de marcadores de AFLP, analisando-se a similaridade genética e identificando-se bandas diferenciadoras entre as mesmas. A partir disso, foi empregada a metodologia de Bulk Segregant Analysis na população F2 de P-152 x DN, para encontrar marcadores AFLP candidatos ao mapeamento do brilho. Foram encontrados marcadores associados que, no entanto, revelaram serem falsos positivos. Análises utilizando marcadores microssatélites ou análises bioinformáticas de sintenia com a soja poderiam ser realizadas, visando detectar marcadores precisamente ligados à característica
Several characteristics interfere in acceptability of common bean varieties (Phaseolus vulgaris L.) by consumers, like seed coat shininess. Generally, varieties with shiny seed coat are rejected by consumers due to their difficult cooking. However, shininess could confer resistance to insects attak and also pathogens to the seed, giving an advantage for this trait in common bean breeding. The presence of shininess is due the expression of the Asp (Asper) gene in the dominant allelic form. Other gene, J (Joker), interferes on the expression of this characteristic, with j conditioning a less shiny seed coat and changing seed coat color. J is considered the precursor of a class of polyfenols called pro-anthocyanidins. In the presence of j these compounds are not synthesized. In the present work we genotyped common bean landraces [Shiny Serro Azul (SAB shiny seed coat) and Dull Serro Azul (SAF dull seed coat) and Puebla-152 (P-152 shiny)] and the cultivar Diamante Negro (DN dull), contrasting for seed coat shininess. Phenotypic, morphological and biochemical analyses allowed to genotype all varieties and evaluate the segregation of shinines in populations derived from crosses between contrasting genotypes: SAF x SAB and P-152 x DN. Results showed that varieties do not vary for J, only for Asp. SAB and P-152 carry Asp and SAF and DN carry asp. In all crosses segregation was of three shiny (Asp) for one opaque (asp) in F2 and of five shiny for three dull in F3. Based on the results, all varities were contrasted by AFLP markers, analyzing genetic similarity and identifying differencial bands among all of them. Further it was used the Bulk Segregant Analysis method in population F2 of the cross P-152 x DN, aiming to find candidate AFLP markers for shininess mapping. We found markers associated but they revealed to be false positives. Further analyses using microsatellite markers or sinteny comparisons with soybean genome could be done, aiming to find specific markers linked to this trait
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Coutinho, Tania Alen. "Caracterização de amostras de Erysipelothrix spp. isoladas de suínos nos últimos 30 anos." Universidade de São Paulo, 2010. http://www.teses.usp.br/teses/disponiveis/10/10134/tde-24032011-152836/.

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Erysipelothrix rhusiopathiae é um importante patógeno em suinocultura e apesar do uso freqüente de vacinas contra o mesmo na maior parte das propriedades produtoras do país, a ocorrência de quadros clínicos da infecção tem sido amplamente observada e diagnosticada. Tendo em vista o ressurgimento deste agente como causa de prejuízos econômicos para a indústria suinícola nacional e seu potencial risco à saúde pública, este estudo teve como objetivo caracterizar 151 amostras de Erysipelothrix spp. isoladas de suínos nos útlimos 30 anos por meio de sorotipagem, determinação da susceptibilidade antimicrobiana, AFLP e PFGE. Dentre os 151 isolados, 139 foram classificados em 18 sorotipos diferentes (1a, 1b, 2a, 2b, 4, 5, 6, 7, 8, 10, 11, 12, 15, 17, 19, 21, 24 e 25), sendo que o sorotipo 2b foi o mais freqüente. Os perfis de susceptibilidade antimicrobiana foram muito semelhantes entre os isolados, o que impossibilitou a subtipagem dos isolados de Erysipelothrix spp. pelos testes de sensibilidade. Dentre os primers testados no AFLP, o HI-G foi o mais adequado à tipagem molecular de Erysipelothrix spp. Apesar do AFLP/HI-G e da PFGE apresentarem o mesmo índice discriminatório (0,98), a PFGE apresentou melhor relação com os dados epidemiológicos que o AFLP/HI-G, tendo em conta os agrupamentos por ela gerados. Independente da técnica molecular empregada, não foi observado a discriminação entre isolados recentes e históricos, bem como um padrão epidemiológico fixo de agrupamento dos mesmos. Contudo, o AFLP/HI-G pode ser uma alternativa interessante para diferenciar as espécies de Erysipelothrix, assim como a PFGE tem grande potencial para agrupar isolados deste gênero de acordo com os sorotipos.
Erysipelothrix rhusiopathiae is an important pathogen in swine production and even with the frequent use of vaccines against it in most of Brazilian pig farms, the occurrence of clinical manifestations of its infection has been widely observed and diagnosed. Given the resurgence of this agent as a cause of economic losses to the national pig industry and its potential risk to public health, this study aimed to characterize 151 samples of Erysipelothrix spp. isolated from swine in last 30 years by serotyping, determination of antimicrobial susceptibility, AFLP and PFGE. Among the 151 isolates, 139 were classified in 18 different serotypes (1a, 1b, 2a, 2b, 4, 5, 6, 7, 8, 10, 11, 12, 15, 17, 19, 21, 24 and 25) and serotype 2b was the most frequent. The susceptibility profiles were very similar among the isolates, which precluded the subtyping of Erysipelothrix spp. isolates by sensitivity tests. Among the primers tested in AFLP, the HI-G was the most suitable for molecular typing of Erysipelothrix spp. Despite AFLP/HI-G and PFGE provided the same discriminatory index (0.98), PFGE presented better relationship with epidemiological data than AFLP/HI-G, given the types of groups generated by it. Regardless of the molecular technique employed, there was no discrimination between recent and historical isolates as well as a fixed epidemiological pattern of grouping them. Nevertheless AFLP/HI-G could be an interesting alternative for Erysipelothrix species discrimination, even as PFGE has a good potential to diferenciate this genus according to serotypes.
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20

Shirahige, Fernando Hoshino. "Avaliação de linhagens de soja derivadas de dois cruzamentos com diferentes níveis de divergência genética." Universidade de São Paulo, 2014. http://www.teses.usp.br/teses/disponiveis/11/11137/tde-11112014-143254/.

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Existem poucas informações relacionadas com a comparação de populações de soja derivadas de cruzamentos com diferentes níveis de divergência genética (DG). Os objetivos deste trabalho foram comparar o desempenho de duas populações de soja derivadas de genitores com baixa e alta DG. Foram realizados dois cruzamentos com genitores diferindo quanto à divergência genética baseada em marcadores moleculares AFLP: baixa DG (IAC-12 x IAC-100) e alta DG (EMBRAPA-60 x EMGOPA-315). Para cada cruzamento foram obtidas 100 progênies F2:3, que foram avaliadas experimentalmente em três ambientes e, posteriormente, selecionadas as 25 progênies mais produtivas. Em seguida foram obtidas 10 linhas puras F5:7 de cada uma das 25 progênies, originando aproximadamente 250 linha puras de cada cruzamento. No ano agrícola 2012/13 foram conduzidos os experimentos de avaliação, utilizando um delineamento em parcelas subdivididas, onde as progênies foram alocadas nas parcelas e as linhas puras dentro de progênies nas subparcelas, e as parcelas arranjadas em um látice balanceado 5x5 (seis repetições). As subparcelas foram constituídas de linhas de 2 m, espaçadas de 0,5 m, contendo 30 plantas após o desbaste. Os caracteres avaliados foram: número de dias para a maturação (DM), altura das plantas na maturação (AM), acamamento (AC) e produção de grãos (PG). A partir da análise de variância foram estimados os seguintes parâmetros para cada cruzamento: média geral, amplitude de variação das médias das linhas puras dentro de progênies, variância genética entre linhas puras dentro de progênies (?^2l/p ), variância fenotípica entre médias de linhas puras dentro de progênies (?^2/ F (l/p) ), coeficiente de herdabilidade entre médias de linhas puras (h ^2/X(l/p) ) e resposta esperada com seleção (Rs). Para todos os caracteres, as médias gerais foram maiores para o cruzamento de maior DG. Para PG, AM e DM as estimativas das variâncias genéticas entre linhas puras dentro de progênies F5:7 foram maiores no cruzamento de maior DG, bem como as amplitudes de variação das médias das linhas puras. Consequentemente, a resposta esperada com seleção entre médias de linhas puras dentro de progênies para PG foi 47,6% maior, em média, bem como a proporção de linhas puras de alta produção, para o cruzamento de maior DG. Os resultados deste trabalho indicam que o uso das medidas de divergência baseada em marcadores moleculares AFLP na escolha de genitores para cruzamentos pode ser uma ferramenta útil para reduzir o número de cruzamentos e, consequentemente, aumentar a eficiência da seleção para produção de grãos em soja.
There is limited information in relation to comparison of populations derived from crosses with different levels of genetic divergence (DG) in soybeans. This work was carried out to compare the performance of two soybean populations derived from parents with low and high DG. From two two-way crosses of soybeans with different levels of AFLP molecular marker genetic divergence (DG): low DG (IAC-12 x IAC-100) and high DG (EMBRAPA-60 x EMGOPA-315), one hundred F2:3 progenies were evaluated in three environments and then selected the 25 high yielding progenies. Ten inbred lines were derived in the generation F5:7 from each of 25 high yielding progeny giving rise to approximately 250 inbred lines for each cross. Evaluation trials were carried out in the 2012/13 growing season, using a split plot design, where progenies were allocated in the plots and inbred lines within progenies in the subplots, and plots arranged according to a 5x5 balanced lattice (six replications). Subplots consisted of 2 m rows spaced by 0.5 m, with 30 plants after thinning. The following traits were recorded: number of days to maturity (DM), plant height at maturity (AM), lodging (AC) and grain yield (PG). The following parameters were estimated: general mean, amplitude of variation of inbred lines within progenies means, genetic variance of inbred lines within progenies ( ?^2 l/p ), phenotypic variance on inbred lines within progenies mean basis ( ?^ 2 F(l/p) ), heritability coefficients on inbred line mean basis ( h ^2 X(l/p) ) and expected response to selection (Rs) on inbred line mean basis. For all traits, general means were higher for the high DG cross. For PG, AM and DM, genetic variance among inbred lines within F5:7 progenies were higher for the high DG cross, as well as the amplitude of variation of inbred line means. As a result, expected response to selection for grain yield (PG) was 47.6% higher, on average, as well as the proportion of high yielding inbred lines for the high DG cross. General results indicate that the use of genetically divergent parents based on AFLP molecular markers for choosing parents for crossings can be useful to reduce the number of crossings, and thus, to improve the efficiency of selection for grain yield in soybeans.
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21

Spindola, Maria Garcia. "Isolamento e caracterização de Campylobacter coli e Campylobacter jejuni em cortes de carne de frango e suíno comercializados na cidade de São Paulo." Universidade de São Paulo, 2017. http://www.teses.usp.br/teses/disponiveis/10/10134/tde-19022018-162759/.

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Atualmente, a campilobacteriose representa uma importante zoonose tanto em países desenvolvidos quanto em países em desenvolvimento. No Brasil, vários estudos relatam a alta frequência de suínos eliminando o agente nas fezes, porém, a contaminação da carne suína comercializada tem sido pouco avaliada, principalmente no que diz respeito à presença de Campylobacter spp. A incidência deste agente em cortes de carne de aves é mais descrita, porém ainda faltam estudos que esclareçam a epidemiologia da doença. Os objetivos principais do presente estudo foram avaliar a presença de Campylobacter spp. em cortes de carne de frangos e suínos vendidos em mercados municipais, açougues e mercados de pequeno porte distribuídos nas cinco regiões do município de São Paulo. Das 115 amostras de origem suína avaliadas sete se mostraram positivas ao isolamento de Campylobacter coli e, das 105 amostras de carne de frango, 31 estavam contaminadas por Campylobacter jejuni ou Campylobacter coli. Dentre as 38 amostras de carne de frango e suíno positivas foram selecionadas 60 estirpes, as quais foram caracterizadas quanto à espécie, utilizando a reação em cadeia pela polimerase e a espectrometria de massa MALDI-TOF, foram ainda avaliadas quanto ao perfil de resistência a antimicrobianos e foram submetidas a genotipagem pelo polimorfismo de comprimento de fragmentos amplificados (AFLP). A partir dos resultados obtidos seis estirpes foram selecionadas para realização do sequenciamento do genoma completo e a partir da análise dos genomas foram identificados os STs, os genes de resistência e genes de virulência.
Currently, Campylobacteriosis represents an important zoonosis in both developed and developing countries. In Brazil, several studies report a high frequency of pigs excreting the agent in the feces, but the contamination of marketed pork has been insufficiently evaluated, especially with regard to the presence of Campylobacter spp. The incidence of this agent in cuts of poultry meat is more detailed; however, there are still studies lacking that clarify the epidemiology of the disease. The main aims of the present study were to evaluate the presence of Campylobacter spp. in chicken and pork cuts sold in municipal markets, butchers and small markets distributed in the five regions of the city of São Paulo. Of the 115 pork samples evaluated, seven were Campylobacter coli isolation positive and 31 of the 105 chicken samples were contaminated with Campylobacter jejuni or Campylobacter coli. Of the 38 chicken and pork positive samples, 60 strains were selected, which were characterized by species using polymerase chain reaction and MALDI-TOF mass spectrometry. They were also assessed for antimicrobial resistance profile and were genotyped by amplified fragment length polymorphism (AFLP). From the results obtained six strains were selected to carry out the complete genome sequencing and from the genome analysis the STs, the resistance genes and the virulence genes were identified.
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22

Sirviö, A. (Anu). "The role of factors promoting genetic diversity within social insect colonies." Doctoral thesis, University of Oulu, 2010. http://urn.fi/urn:isbn:9789514262074.

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Abstract The evolution of sociality is often associated with close relatedness and genetic similarity of interacting individuals. However, colonies of advanced social insects (e.g. ants, bees and wasps) characterized by large colony size and division of tasks, are also shaped by acquisition of genetic diversity by polyandry, polygyny, recombination and even by hybridization. The balance between forces selecting for high relatedness on one hand and for improved colony performance though increased genetic diversity on the other hand forms an intriguing area of research. My study has produced the first genetic linkage maps for ants (Acromyrmex echinatior and Pogonomyrmex rugosus) and social wasps (Vespula vulgaris). Together with the findings of earlier honeybee research, it is shown that advanced eusocial insects have higher recombination rates than any other insect (or animal) studied so far. The estimates obtained here were 14 cM/Mb for P. rugosus, 9.7 cM/Mb for V. vulgaris and 6.2 cM/Mb for A. echinatior. Pogonomyrmex harvester ants have a genetic caste determination system in which workers arise from mating between two hybridizing lineages whereas sexuals are produced by within-lineage mating. I evaluated the origin of the lineages and the caste determination system by using 751 variable nuclear genetic markers. Fertile hybrids would lead to introgression, particularly in genomic regions characterized by a high recombination rate and lack of strongly selected loci. The hybridizing lineages (lineage pairs J1/J2 and H1/H2) showed many fixed differences. Nineteen of them were in the constructed linkage map, scattered in different linkage groups. The results suggest that there has been no recent introgression. As the hybrids are viable (as workers), caste differentiation can be affected by many loci scattered throughout the ant genome or by a small number of very strongly selected loci. Genetic diversity in colonies of the ant Formica cinerea is affected by varying levels of polygyny. I tested the hypotheses that the prevalence of endosymbiotic bacteria can vary in polygynous colonies but be either very low or very high in monogynous colonies. However, I found no association between the level of polygyny and endosymbiont prevalence. In addition to Wolbachia, I found two other endosymbiotic bacteria Cardinium and Candidatus Serratia symbiotica which have not been earlier reported from ants. Genetic diversity in insect colonies is affected by polyandry and polygyny. My results indicate that high a recombination rate is also an important factor influencing diversity. Genotypically diverse progenies can enhance colony success, e.g. through effects on division of labour or defence against pathogens. Recombination differs from the other factors in its effects on genetic relatedness among colony members.
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23

Tero, N. (Niina). "Genetic structure at different spatial scales in metapopulations of Silene tatarica." Doctoral thesis, University of Oulu, 2005. http://urn.fi/urn:isbn:9514277694.

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Abstract The genetic structure at different spatial scales and growing habitats was studied on Silene tatarica, using AFLP and microsatellite markers. S. tatarica is a rare perennial plant occurring along riverbanks and shores of two annually flooding rivers in Finland. Regional scale analysis based on AFLP fragment analysis showed that at Oulanka River population structure represented mostly classical metapopulation model. In general, colonization-extinction processes had an important role, dispersal between subpopulations was limited and genetic differentiation was independent of geographic location. The same subpopulations were partly used to study spatial genetic structuring within subpopulations. Spatial autocorrelation revealed clear spatial genetic structure in each subpopulation. Paternity analysis in an isolated subpopulation showed small amounts of inbreeding, restricted seed dispersal and pollen flow through the subpopulation. Factors affecting the creation and maintenance of spatial genetic structure within subpopulation were most likely colonization events and restricted seed dispersal. The impact of river regulation on the genetic structure of populations was studied by comparing results from Oulanka River to the results obtained from second main growing area, Kitinen River. Oulanka River is a natural river system, whereas Kitinen is a regulated river. The overall regional scale studies did not indicate major differences between river systems. There were some clear population genetic differences between rivers but there were no clear evidence that those would have been caused by river regulation. More likely differences were related to the marginal location of Kitinen population at the edge of the distribution range. Studies indicated that regardless of the species rarity in Finland, active management measures are not currently needed in either S. tatarica growing area. Species specific microsatellite loci were isolated to complement AFLP studies. During the microsatellite isolation, an interesting amplification pattern was detected and studied further. It was suggested that there were repetitive areas within genome containing microsatellites resulting in unusual amplification. The most likely explanation for this phenomenon would be transposable elements containing proto-microsatellite areas. The microsatellites isolated could have evolved mostly from those proto-microsatellites.
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24

Qubbaj, Tawfiq A. H. "Physiological and molecular responses of resistant and susceptible apple cultivars of Malus domestica L. to the Rosy apple aphid, Dysaphis plantaginea (Passerini)." Beuren Stuttgart Grauer, 2005. http://d-nb.info/989884813/04.

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25

Rodrigues, Maria Gabriela Fontanetti [UNESP]. "Caracterização genética de seleções irradiadas de figueira por marcadores moleculares (RAPD e AFLP)." Universidade Estadual Paulista (UNESP), 2010. http://hdl.handle.net/11449/96965.

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Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)
A figueira (Ficus carica L.) é uma frutífera de grande importância mundial e, neste sentido, o melhoramento genético se torna uma linha de pesquisa importante para a melhoria da cultura, sendo necessário reunir informações sobre esta espécie, principalmente em relação à sua variabilidade genética, para que projetos de propagação e manejo adequados sejam realizados. O presente trabalho teve como objetivo verificar a existência de variabilidade genética, por marcadores moleculares RAPD e AFLP, de seleções originadas de estacas provenientes de gemas irradiadas com raio gama. O experimento foi conduzido na Faculdade de Ciências Agrárias e Veterinárias - UNESP - Campus de Jaboticabal - SP, utilizando-se estacas de cinco seleções de figueira obtidas em trabalho anterior realizado na Faculdade de Engenharia de Ilha Solteira - UNESP, comparando-as entre si e utilizando a cultivar Roxo-de- Valinhos como parâmetro de comparação. Não há polimorfismo entre os tratamentos, indicando uma possível variação epigenética, devendo ser testada com outras técnicas sensíveis à uma possível metilação do DNA
The fig (Ficus carica L.) is a fruit of great importance worldwide and in this sense, the genetic improvement becomes an important line of research to improve the culture, it is necessary to gather information about this species, especially in relation to their variability gene for propagation projects and handling are carried out. This study aims to determine the existence of genetic variability of selections originated from cuttings from buds irradiated with gamma rays, using the RAPD and AFLP molecular markers. The experiment was conducted at the Faculdade de Ciências Agrárias e Veterinárias - UNESP - Jaboticabal - SP, using cuttings from five fig selections obtained in a previous study conducted at the Faculdade de Engenharia de Ilha Solteira - UNESP, comparing them with each other and using the Roxo-de-Valinhos cultivar for comparison. There was no polymorphism between treatments, indicating a possible epigenetic variation and should be tested with other techniques sensitive to a DNA methylation
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26

Molin, Dayane. "DIVERSIDADE GENÉTICA EM MILHO CRIOULO ATRAVÉS DOS MARCADORES MOLECULARES RAPD, MICROSSATÉLITE E AFLP." UNIVERSIDADE ESTADUAL DE PONTA GROSSA, 2012. http://tede2.uepg.br/jspui/handle/prefix/953.

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Fundação Araucária de Apoio ao Desenvolvimento Científico e Tecnológico do Paraná
The wide variability in corn is due to the numerous landraces, important genotypes for breeding programs, because they constitute a source of genetic variability in the exploration of new genes of economic interest. The objectives were to analyze the genetic diversity between landraces from Rio Grande do Sul and Paraná through the analysis of polymorphism generated by RAPD, microsatellite (SSR) and AFLP markers; cluster these genotypes through estimates of genetic similarity and establish possible relationships between genetic similarity and the sampling sites of the landraces. PCR reactions for each marker were optimized through specific protocols being used: 30 RAPD primers, 47 SSR primers pairs and 25 combinations of primers for the EcoRI + MseI for the AFLP marker. The amplified fragments (RAPD and SSR) were visualized in agarose gel at 2 and 3 %, respectively, through horizontal electrophoresis run for approximately 4 h at 80 V. The AFLP amplification products were resolved on a polyacrylamide gel (6 %) submitted to a vertical electrophoresis run for 3 h 30 min at 80 W (1500 V). Genotyping of the varieties of corn with the RAPD marker amplified 409 fragments with a polymorphism average rate of 81.9 %. The SSR generated 134 fragments with 78.3 % of polymorphism. On the other hand, the AFLP amplified 1889 fragments with a polymorphism average rate of only 40.3 %. The polymorphic fragments were submitted to analysis of genetic similarity using the Jaccard coefficient and UPGMA clustering method individually and jointly for all markers. The coefficient mean of similarity was 57 % for RAPD, 56 % for SSR, 74 % for the AFLP and 69 % for the joint analysis. The dendrograms obtained from RAPD and SSR showed 8 different groups, while the dendrogram obtained from AFLP and the joint analysis formed six and seven groups, respectively. In general, the correlations between the similarity matrices were low, but between the AFLP and combined analysis was 96 %. Results revealed a wide genetic variability among landraces. The RAPD and SSR had the highest average rates of polymorphism and AFLP showed the highest rates of genetic similarity among landraces. In general, the markers used were effective tools for sampling the genetic diversity and cluster varieties according to the sampling sites, although they have differential capacity to reveal polymorphism as well as to cluster the landraces.
A ampla variabilidade existente em milho deve-se às inúmeras variedades crioulas, genótipos importantes para o melhoramento, pois constituem fonte de variabilidade genética na prospecção de novos genes de interesse econômico. Os objetivos deste trabalho foram analisar a diversidade genética existente entre acessos de milho crioulo oriundos do Rio Grande do Sul e do Paraná a partir da análise do polimorfismo gerado pelos marcadores RAPD, microssatélite (SSR) e AFLP; realizar o agrupamento destes genótipos através das estimativas da similaridade genética e estabelecer possíveis relações entre a similaridade genética e os locais de coleta das variedades crioulas. As reações de PCR para cada marcador foram otimizadas através de protocolos específicos, sendo utilizados: 30 primers RAPD, 47 pares de primers SSR e 25 combinações de primers EcoRI + MseI para o marcador AFLP. Os fragmentos amplificados (RAPD e SSR) foram visualizados em gel de agarose a 2 e 3 %, respectivamente, através de corrida eletroforética horizontal por aproximadamente 4 h a 80 V. Os produtos da amplificação do AFLP foram resolvidos em gel de poliacrilamida (6 %) submetidos à corrida eletroforética vertical por 3 h e 30 minutos a 80 W (1500 V). A genotipagem das variedades de milho com o marcador RAPD amplificou 409 fragmentos com índice médio de polimorfismo de 81,9 %. O SSR gerou 134 fragmentos com 78,3 % de polimorfismo. Por outro lado, o AFLP amplificou 1889 fragmentos com índice médio de polimorfismo de apenas 40,3 %. Os fragmentos polimórficos foram submetidos às análises de similaridade genética através do coeficiente de Jaccard e de agrupamento pelo método UPGMA individualmente e conjuntamente para os marcadores. O coeficiente médio de similaridade foi de 57 % para o RAPD; 56 % para o SSR; 74 % para o AFLP e 69 % para a análise conjunta. Os dendogramas obtidos a partir do RAPD e SSR mostraram 8 grupos distintos, enquanto que o dendograma obtido a partir do AFLP e da análise conjunta formaram 6 e 7 grupos, respectivamente. De maneira geral, as correlações entre as matrizes de similaridade foram baixas, porém entre o AFLP e a análise conjunta foi de 96 %. Os resultados revelaram ampla variabilidade genética entre os acessos de milho crioulo. Os marcadores RAPD e SSR apresentaram os maiores índices médios de polimorfismo e o AFLP demonstrou maiores índices de similaridade genética entre os acessos crioulos. De maneira geral, os marcadores utilizados foram ferramentas eficientes para amostrar a diversidade genética e agrupar as variedades de acordo com os locais de coleta, embora possuam capacidade diferencial de revelar polimorfismo bem como para agrupar os acessos crioulos de milho.
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27

Rodrigues, Maria Gabriela Fontanetti. "Caracterização genética de seleções irradiadas de figueira por marcadores moleculares (RAPD e AFLP) /." Jaboticabal : [s.n.], 2010. http://hdl.handle.net/11449/96965.

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Resumo: A figueira (Ficus carica L.) é uma frutífera de grande importância mundial e, neste sentido, o melhoramento genético se torna uma linha de pesquisa importante para a melhoria da cultura, sendo necessário reunir informações sobre esta espécie, principalmente em relação à sua variabilidade genética, para que projetos de propagação e manejo adequados sejam realizados. O presente trabalho teve como objetivo verificar a existência de variabilidade genética, por marcadores moleculares RAPD e AFLP, de seleções originadas de estacas provenientes de gemas irradiadas com raio gama. O experimento foi conduzido na Faculdade de Ciências Agrárias e Veterinárias - UNESP - Campus de Jaboticabal - SP, utilizando-se estacas de cinco seleções de figueira obtidas em trabalho anterior realizado na Faculdade de Engenharia de Ilha Solteira - UNESP, comparando-as entre si e utilizando a cultivar Roxo-de- Valinhos como parâmetro de comparação. Não há polimorfismo entre os tratamentos, indicando uma possível variação epigenética, devendo ser testada com outras técnicas sensíveis à uma possível metilação do DNA
Abstract: The fig (Ficus carica L.) is a fruit of great importance worldwide and in this sense, the genetic improvement becomes an important line of research to improve the culture, it is necessary to gather information about this species, especially in relation to their variability gene for propagation projects and handling are carried out. This study aims to determine the existence of genetic variability of selections originated from cuttings from buds irradiated with gamma rays, using the RAPD and AFLP molecular markers. The experiment was conducted at the Faculdade de Ciências Agrárias e Veterinárias - UNESP - Jaboticabal - SP, using cuttings from five fig selections obtained in a previous study conducted at the Faculdade de Engenharia de Ilha Solteira - UNESP, comparing them with each other and using the Roxo-de-Valinhos cultivar for comparison. There was no polymorphism between treatments, indicating a possible epigenetic variation and should be tested with other techniques sensitive to a DNA methylation
Orientador: Antonio Baldo Geraldo Martins
Coorientadora: Janete Apparecida Desidério
Banca: Luiz de Souza Corrêa
Banca: Bianca Waléria Bertoni
Mestre
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28

Paula, Gabriela Barbosa Navarro de. "Estudos em Hypochaeris tropicalis Cabrera (Asteraceae) utilizando marcadores moleculares AFLP, SSR e ITS." Universidade Estadual de Londrina, Instituto Agronômico do Paraná, EMBRAPA. Centro de Ciências Biológicas. Programa de Pós-Graduação em Genética e Biologia Molecular, 2015. http://www.bibliotecadigital.uel.br/document/?code=vtls000204131.

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Hypochaeris tropicalis é uma espécie com distribuição restrita a poucas áreas, na região sudoeste do Rio Grande do Sul (Brasil), com umas poucas informações de ocorrência na Argentina e Uruguai. A fim de determinar a estrutura genética de populações desta espécie e a sua posição filogenética dentro do grupo sul-americano do gênero, foram utilizados marcadores moleculares AFLP (Amplified Fragment Length Polymorphism), microssatélites-SSR (Simple Sequence Repeats) e sequências de ITS (Internal Transcribed Spacer). Para o estudo de populações seis combinações de primers seletivos de AFLP e nove pares de primers de SSR foram aplicados em seis populações de H. tropicalis. A técnica de AFLP possibilitou a identificação de 1.488 marcadores, com uma média de 67% de polimorfismo. Foi identificado um total de 56 alelos com uma média de 6,2 alelos por loco nas seis populações. Ambos, AFLP e SSRs, idenficaram uma maior variação dentro (91,06 e 97,08) do que entre (8,94 e 2,92) as populações investigadas, sugerindo que a espécie possui um sistema reprodutivo por fecundação cruzada ou mista. Foi identificada uma baixa estruturação genética, possivelmente devido à diversificação rápida e recente do gênero Hypochaeris na América do Sul. Para definir a posição filogenética de H. tropicalis dentro do grupo sul-americano de Hypochaeris, foram utilizadas sequências de regiões ITS (Internal Transcribed Spacer) e três primers seletivos de AFLP. Nesta investigação foram analizadas oito espécies nativas da América do Sul, além de H. angustifólia, possível ancestral do grupo e duas espécies europeias como outgroups (ITS). Os dados de AFLP identificaram 1.213 marcadores com 88% de polimorfismo enquanto que as sequências ITS geraram 643 caracteres onde, somente 13,7% foram informativos. Os marcadores AFLP e sequências ITS possibilitaram a inserção de H. tropicalis na filogenia de Hypochaeris na América do Sul.
Hypochaeris tropicalis is a species with restrict distribution in southeast of Rio Grande do Sul state in Brasil, with a few reports in Argentina and Uruguay. This study aim to determine the population genetic structure of the species, as well as to define the phylogenetic position of the species within the South American Hypochaeris. For this purpose we used AFLPs (Amplified Fragment Length Polymorphism), microsatellites (SSR-Simple Sequence Repeats) and ITS (Internal Transcribed Spacer) sequences. Six AFLP primer combinations and nine SSR primer pairs were applied for population studies. The AFLP technique allowed the identification of 1,488 markers, with an average of 67% of polymorfism. PCR amplification of the nine SSR loci idenfied a total of 56 aleles and an average of 6,2 aleles per locus. Both, AFLP and SSRs, idenfied higher variation (91,06 e 97,08) within than amog (8,94 e 2,92) populations, suggesting that H. tropicalis is predominantly alogamous. The population genetic structure of the species was low, possibly because of the recent colonization and diversification of the genus in the South American continent. ITS sequences and AFLP markers were also used to define the phylogenetic position of H. tropicalis. For this purposes eight species native to South America, H. angustifólia, the presumed ancestor of the group, and two European species (outgroups) were investigated. Three AFLP primer combinations identified 1.213 markers with 88% of polymorphism while the ITS sequences rendered 643 characters but, only 13.7% were informative. The AFLP data and ITS sequences allowed the insertion of the phylogeny of H. tropicalis Hypochaeris in South America.
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29

Gomes, Vasco Tulio de Moura. "Caracterização genotípica e fenotípica de cepas de Escherichia coli associadas à doença do edema em suínos." Universidade de São Paulo, 2013. http://www.teses.usp.br/teses/disponiveis/10/10134/tde-13062013-102027/.

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A doença do edema afeta os leitões desmamados e é causada por cepas de Escherichia coli adaptadas ao hospedeiro e produtoras da toxina Stx2e. A doença do edema é caracterizada por edema de pálpebras, ataxia, pedalagem, dificuldade locomotora, e morte súbita. No presente estudo foram avaliadas 158 cepas de E. coli positivas para presença do gene codificador da toxina Stx2e isoladas de 62 animais provenientes de 13 granjas localizadas nos Estados do Rio Grande do Sul, Santa Catarina, Mato Grosso, Paraná, São Paulo, Goiás e Minas Gerais. As cepas foram submetidas a determinação do perfil de resistência, caracterização dos genes de virulência, determinação do grupo filogenético, expressão da toxina em cultivos de célula Vero, caracterização genotípica através da eletroforese em campo pulsado (PFGE) e polimorfismo do comprimento de fragmentos amplificados com uma única enzima (SE-AFLP). Dentre as 158 cepas stx2e+ foram identificadas 83,5% (132/158) apresentando resistência a três classes de antimicrobianos ou mais. Altos níveis de resistência forma identificados contra tetraciclina, sulfonamidas e florfenicol. A frequência dos genes de virulência associados a doença do edema como a fímbria F18, por exemplo, foi baixa em relação a outros estudos. Todas as 158 cepas testadas apresentaram a expressão da toxina e efeito citotóxico em células Vero. A caracterização dos grupos filogenéticos permitiu a distribuição das cepas nos quatro grupos descritos a seguir: grupo A 27,2% (43/158), grupo B1 3,8% (6/158), grupo B2 39,2% (62/158) e grupo D 29,8% (47/158). As cepas foram caracterizadas através da PFGE e do SE-AFLP e ambas as técnicas apresentaram altos índices discriminatórios (0,98 e 0,99 respectivamente). A associação mais frequente nas duas técnicas genotípicas foi observada em relação ao animal e a granja de origem. Apesar de pertencerem a um patotipo definido (STEC) e de serem altamente especializadas em relação ao hospedeiro, o suíno, foi observada uma grande variabilidade genética e de perfis de resistência entre as cepas de E. coli estudadas.
Edema disease affects weaning piglets and is caused by a host adapted Escherichia coli and producer of Stx2e toxin. The edema disease is characterized by swollen eyelids, ataxia, recumbence, convulsions, paralysis, or sudden death. In the present study were evaluated 158 E. coli strains Stx2e toxin gene positive isolated from 62 animals, from 13 swine herds located at Rio Grande do Sul, Santa Catarina, Mato Grosso, Paraná, São Paulo, Goiás and Minas Gerais States. Strains were submitted to resistance profile determination, virulence genes detection, phylogenetic group characterization, toxin expression in Vero cell culture, genotypic characterization through pulsed field gel electrophoresis (PFGE) and single enzyme amplified fragments length polymorphism (SEAFLP). Among the 158 strains stx2e+ were identified 83.5% (132/158) resistant to more than three or more classes of antimicrobials, High levels of resistance were found against tetracycline, sulfonamide and florfenicol. The frequency of virulence genes associated to edema disease as F18 fimbriae, for example, was low in relation to other studies. All 158 tested strains presented Stx2e toxin expression and cytotoxic effect in Vero cell culture. The characterization of phylogenetic groups permitted the distribution of strains in four groups described as follow: group A 27.2% (43/158), group B1 3.8% (6/158), group B2 39.2% (62/158) and group D 29.8% (47/158). The strains were characterized through PFGE and the SE-AFLP, and both techniques presented high discriminatory index (0.98 and 0.99 respectively). The association more frequently in both techniques was observed in relation to animal and herd origin. Despite to belong to one defined pathotype (STEC) and to be highly specialized in relation to host, the swine, it was observed a high variability of genetic and resistance profile among tested E. coli.
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30

Gobbi, Débora Dirani Sena de. "Caracterização fenotípica e genotípica de isolados de Arcobacter spp. provenientes de suínos." Universidade de São Paulo, 2013. http://www.teses.usp.br/teses/disponiveis/10/10134/tde-08092014-150431/.

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Dentre as espécies conhecidas do gênero Arcobacter, as espécies A. butzleri, A. cryaerophilus e A. skirrowii são consideradas potecialmente zoonóticas, podendo ser transmitidas por alimentos de origem animal. O presente estudo teve como objetivos isolar e caracterizar fenotipica e genotipicamente cepas de Arcobacter spp. provenientes de carcaças de suínos e amostras de ambiente de abatedouro localizado no Estado de São Paulo. As cepas isoladas foram submetidas a reação em cadeia pela polimerase para a identificação e detecção de um grupo de genes de virulência. A concentração inibitória mínima frente a nove antimicrobianos usados para o controle da infecção pelo agente foi determinada e as cepas foram analisadas através do PFGE e pelo AFLP. Dentre as 30 carcaças avaliadas, 25 foram positivas para o agente e 70 cepas foram selecionadas e identificadas como Arcobacter spp. As espécies isoladas foram A. butzleri (n=61), A. cryaerophilus (n=7) e A. skirrowii (n=2). A frequência dos possíveis genes de virulência encontrada variou de 71,4% a 100% para os genes tlyA, pldA, cj1349, ciaB, cadF e mviN. Não foram detectados os genes hecA, hecB e irgA. O perfil de virulência ciaB/ cj1349/ mviN/ cadF/ pldA/ tlyA foi o mais frequente e detectado em 66% das cepas. Todas as cepas foram sensíveis à gentamicina e tetraciclina e 77,1% foram multirresistentes, dentre estas o perfil mais frequente foi de resistência a azitromicina/ florfenicol/ ácido nalidíxico/ telitromicina/ clindamicina Houve grande diversidade genotípica entre as cepas através do PFGE e do AFLP, e ambas a técnicas apresentaram o mesmo poder discriminatório na análise das cepas isoladas.
Among the known species of the genus Arcobacter, the species A. butzleri, A. cryaerophilus and A. skirrowii are considered potentially zoonotic and can be transmitted by food of animal origin. This study aimed to isolate and characterize phenotypically and genotypically strains of Arcobacter spp from swine carcasses and slaughterhouse environment samples located in the State of São Paulo. The isolated strains were subjected to polymerase chain reaction for identification and detection of a group of putative virulence genes. The minimum inhibitory concentration was determined against nine antimicrobials indicated for the control of infection by the agent and the strains were analyzed by PFGE and by AFLP. Among the 30 carcasses evaluated, 25 were positive for the agent and 70 strains were selected and identified as Arcobacter spp. The isolated species were A. butzleri (n = 61), A. cryaerophilus (n = 7) and A. skirrowii (n = 2). The frequency of virulence genes found ranged from 71.4 % to 100 % for genes tlyA , pldA , cj1349 , ciaB , cadF and mviN . The genes hecA, hecB and irgA were not detected. The virulence profile ciaB/ cj1349/ mviN/ cadF/ pldA/ tlyA was the most frequent and detected in 66 % of the strains. All strains were susceptible to gentamicin and tetracycline and 77.1% were multirresistant, among these the most common profile of resistance was azithromycin/ florfenicol/ nalidixic acid/ telithromycin/ clindamycin There were large genotypic diversity among strains by PFGE and AFLP and both techniques showed the same discriminatory power in the analysis of the isolated strains.
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31

Amigo, Cristina Román. "Desenvolvimento da reação em cadeia pela polimerase para detecção de Actinobaculum suis e caracterização fenotípica e genotípica dos isolados." Universidade de São Paulo, 2012. http://www.teses.usp.br/teses/disponiveis/10/10134/tde-21052013-151439/.

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O Actinobaculum suis é um dos principais micro-organismos relacionados a infecções de trato urinário em fêmeas suínas. As características de crescimento deste agente dificultam o isolamento bacteriano tradicional, o que pode tornar a sua prevalência subestimada. Este estudo teve por objetivos desenvolver a reação em cadeia pela polimerase (PCR) para detecção do A. suis, avaliar a sensibilidade e especificidade desta técnica e comparar seu desempenho com o isolamento bacteriano. Além disso, as cepas isoladas foram caracterizadas através do polimorfismo de comprimento de fragmentos amplificados (AFLP) e submetidas à determinação da concentração inibitória mínima para caracterização dos perfis de susceptibilidade antimicrobiana. Foram analisados 45 suabes prepuciais de machos e 192 urinas de fêmeas suínas provenientes de três granjas. Os resultados indicaram que a PCR desenvolvida foi específica para o A. suis e apresentou limiar de detecção entre 1,0 X 101 UF/mL e 1,0 X 102 UFC/mL. A frequência de A. suis encontrada através da PCR foi de 82,2% (37/45) nos suabes prepuciais e de 8,9% (17/192) nas urinas de fêmeas. No que se refere ao isolamento, nenhuma das amostras de urina foi positiva para o agente, enquanto 31,1% (14/45) dos suabes foram positivos. A partir das amostras positivas isoladas dos suabes prepuciais foram selecionadas 20 cepas de A. suis. Os perfis de susceptibilidade entre estas cepas foram semelhantes, no entanto diferiram dos isolados utilizados como controle e provenientes de uma fêmea com infecção urinária. A técnica de PCR foi mais eficiente que o isolamento na identificação de amostras positivas para A. suis. Através do AFLP com uma única enzima foi possível caracterizar todos os isolados e relacionar os dados obtidos com a origem das cepas e o perfil de resistência. Até o presente não há relatos na literatura de caracterização genotípica de A. suis através do AFLP ou detecção do agente através da PCR.
Actinobaculum suis is an important agent related to urinary infection in swine females. The growth characteristics of this agent hamper the traditional bacterial isolation, which can make their prevalence underestimated. The purpose of this study was to develop the polymerase chain reaction (PCR) for Actinobaculum suis detection, to evaluate the sensitivity and specificity of this technique and compare the results with bacterial isolation. Moreover, the isolates were characterized by amplified fragment length polymorphism (AFLP) and subjected to determination of minimum inhibitory concentration for characterization of the antimicrobial susceptibility profiles. Forty-five preputial swabs from boars and a hundred and ninety-two urine samples from sows of three herds were analyzed. The results indicate that the developed PCR was specific for A. suis, presenting a limit detection between 1.0 X 101 UFC/ml and 1.0 X 102 UFC/ml. A.suis frequency by PCR was 82.2% (37/45) in male preputial swabs and 8.9% (17/192) in females urine. Through traditional isolation, none of the urine samples were positive, while A.suis growing was observed in 31.1% (14/45) of the swabs. From the positive samples of the preputial swabs were selected 20 A.suis strains. The susceptibility profiles among these strains were similar, but differed from the female isolates used as control. The PCR technique was more effective than isolation for the A.suis detection. The AFLP with a single enzyme was able to characterize all isolates and relate the data obtained with the strains origin and resistance profile. Until present, there are no reports of genotypic characterization of A. suis strains through AFLP or agent detection by PCR.
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32

Rahman, M. A. "Analysis of the sex chromosomes and autosomes of rumex acetosa by AFLP and cytology." Thesis, Imperial College London, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.271509.

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33

Patel, Simit. "Local adaptation in the land snail, Cepaea nemoralis : exploratory genetic analysis with AFLP markers." Thesis, University of Reading, 2012. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.559281.

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The polymorphic land snail, Cepaea nemoralis (L.) shows a higher prevalence of yellow, banded shells in open habitats and non-yellow (Pink and brown), unbanded shells in woodland. Shell characters are genetically controlled and this pattern of local adaptation is geographically repeated, implying selection is operating. However, no molecular evidence exists to support this claim. An FSI-outlier approach revealed six AFLP loci with elevated levels of differentiation compared to neutral expectations - three in one open-woodland population pair and another three in another pair - providing evidence of positive selection operating between open and woodland habitats. The non-repeated nature of outliers suggests tlie two sites are adapting to habitats by different strategies. Pairwise F SI and a neighbour-joining tree show the two study sites to be genetically divergent from each other, probably because they are geographically isolated (~60km apart) and there are low levels of differentiation between habitats within each pair. An attempt was made at creating a preliminary AFLP linkage map for C. nemoralis using a pseudo-testcross design. A mapping population segregating for shell colour and mid-banding was established but only three, small AFLP linkage groups were identified in one of the parental maps and none in the other. This was largely due to a small proportion of loci being in testcross configuration. In addition, morph frequency data were compared to historic records to look for changes in morph/allele frequency over time. All open populations showed significant differences in colour or banding, whereas no significant differences were found in any woodland populations. This could be an adaptive response to differences in habitat stability between open and woodland, the latter being more stable. Alternatively, balancing selection could be operating in woodlands and open populations fluctuate randomly. The difference in morph frequency stability between habitats was not reflected in allele frequency changes (assuming Hardy-Weinberg equilibrium). 1.
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34

Quadri, Asima. "Assessment of genetic diversity in Asarum canadense L. using amplified fragment length polymorphism (AFLP)." Virtual Press, 2007. http://liblink.bsu.edu/uhtbin/catkey/1371851.

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Forest fragmentation poses a serious danger to population diversity in plants and animals by increasing species isolation, thus reducing the population size and genetic diversity. However, little information is available concerning how fragmentation impacts plant diversity. AFLP fingerprinting was used to assess genetic diversity within and between populations of Asarum canadense L. (Canadian Wild Ginger) across 11 different populations in East-Central Indiana. AFLP fingerprints using two primer pairs generated 51 distinct bands with an average of 25.5 bands per primer. Forty-eight low molecular weight distinct polymorphic bands were observed (50-200 bp range). The percentage of polymorphism was low (0-25%) indicating low levels of genetic diversity within each population studied. NTSYSpc Numerical Taxonomy Analysis Software generated aphenogram that revealed high levels of homologies within populations (75-100%), with individuals from the same population typically clustered. The genetic diversity between populations ranged from 10-50%. The populations from Jay, Randolph and Henry Counties clustered together exhibiting -54% homology, while populations from Mien, Madison, and Huntington counties shared approximately 64% homology. The populations from Adams, Blackford, Delaware, and Grant counties shared approximately 66% homology. However, within this last group Blackford and Delaware counties shared 90% homology. There were no apparent effects of the size of the forest fragments on the observed diversity measures. A possible relationship between genetic diversity and spatial distance was observed between populations moving from east to west. Possible reasons for this observation may be due to forest types, age of forests, climatic factors, soil types, and/or anthropogenic activities. Overall, the low level of average diversity within the populations strongly suggests that the individuals inhabiting isolated forests primarily propagate by asexual means.Ball State UniversityMuncie, IN 47306
Department of Biology
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35

Palhares, Alessandra Carolina. "Mapeamento genético de marcadores AFLP e de retrotransposons em cana-de-açúcar (Saccharum spp.)." Universidade de São Paulo, 2010. http://www.teses.usp.br/teses/disponiveis/11/11137/tde-24052010-105229/.

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No presente trabalho, AFLPs e marcadores baseados em retrotransposons foram utilizados para a construção de um mapa de ligação integrado em cana-de-açúcar. Dois retrotransposons encontrados no genoma da cana-de-açúcar, denominados SURE e Garapa, foram estudados. Os princípios da técnica NBS-profiling foram usados para gerar marcadores direcionados às sequências desses retrotransposons. Os marcadores foram analisados numa população F1 de cana-de-açúcar, composta por 188 indivíduos, oriunda do cruzamento entre os genitores IAC66-6 e TUC71-7. O mapa integrado foi construído usando-se o software OneMap, especialmente desenvolvido para mapear espécies não endogâmicas. Excelentes padrões de AFLP e de marcas direcionadas ao retrotransposon SURE foram obtidos; entretanto, para o Garapa, ainda são necessários ajustes na técnica. Um total de 600 marcadores de dose única foi obtido a partir de 22 combinações de enzimas de restrição/primers de AFLP e seis combinações otimizadas para amplificar marcas direcionadas ao retrotransposon SURE. Construiu-se um mapa com 107 grupos de ligação, com tamanho de 4.316,5 cM e densidade de 8,74 cM/marcador. O mapeamento dos marcadores derivados do retrotransposon SURE revelou que esse elemento não está uniformemente distribuído nos grupos de ligação e confirmou o seu baixo número de cópias no genoma da cana, conforme foi sugerido na literatura.
In the presenty study, AFLPs and retrotransposon-based markers were used for the construction of an integrated linkage map of sugarcane. Two retrotransposons described in the sugarcane genome, named SURE and Garapa were studied. The principles of NBS-profiling technique were used to generate markers based on these retrotransposon sequences. The markers were analyzed in a F1-population, composed of 188 individuals, derived from a single cross between the IAC66-6 and TUC71-7 parents. The integrated genetic map was constructed using the software OneMap, specially designed for mapping outcrossing species. Excellent gel profiles of AFLP and retrotransposon-derived markers were obtained; however, for the Garapa element, technical adjustments are still needed. A total of 600 single-dose markers were obtained from 22 AFLP restriction enzyme/primer combinations and six combinations optimized to amplify the SURE-based markers. A map with 107 linkage groups was constructed, spanning 4,316.5 cM, with a marker density of 8.74 cM. Mapping of SURE-based markers revealed that this element is not uniformly distributed across the linkage groups, and confirmed its low copy number in the sugarcane genome, as suggested in the literature.
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36

Maia, Thiago Andrade. "Análise da estrutura genética da população de Hemileia vastatrix com base no marcador AFLP." Universidade Federal de Viçosa, 2009. http://locus.ufv.br/handle/123456789/4373.

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Obtaining coffee plants with durable resistance to coffee rust has been hindered by the lack of information about the evolutionary potential of Hemileia vastatrix. Seeking to give subsidies to the breeding program, the population structure of H. vastatrix was analyzed based on AFLP markers. To do this, 91 pathogen isolates were collected in genotypes from Coffea arabica, C. canephora, Híbrido de Timor and Icatu derivatives cultivated in the main production regions in Brazil. After the selective amplification using four primer combinations (EcoRI/MseI), 100 polymorphic fragments were analyzed. Each isolate presented a unique pattern of AFLP alleles, accounting for a high genotype diversity. The genetic similarity between the H. vastatrix isolates ranged from 0.08 to 0.70 and no cluster formations were observed in the dendrogram. There was no correlation between genetic and geographical distance between the isolates (r = 0.307, P = 0.234). H. vastatrix isolates were separated based on the host in three populations (Coffea arabica, C. canephora and Híbrido de Timor/Icatu derivates) and low genetic differentiation (GST = 0.026) was observed among them. After analyzing the populations, subdivided based on their geographical area, the genetic diversity (HT, HS and GST) showed no significant difference among the populations and based on AMOVA it was verified that a genetic variance (99.56%) exists within the pathogen populations. The analysis of the number of migrants (Nm) revealed a high gene flow rate among the populations originating from different hosts. The association index showed that the hypothesis of random mating was not rejected among H. vastatrix isolates from the C. canephora population (IA = 0.15, P = 0.18). The presented results show that H. vastatrix populations are not consistent with clonal reproduction indicating a high evolutionary potential, which would have direct implications in handling this pathosystem, mainly in the variety with durable resistance obtained.
A obtenção de cafeeiros com resistência durável à ferrugem tem sido dificultada pela carência de informação sobre o potencial evolutivo de Hemileia vastatrix. Visando dar subsídios ao programa de melhoramento, a estrutura genética da população de H. vastatrix foi analisada com base no marcador AFLP. Para isso, amostrou-se 91 isolados do fungo em genótipos de Coffea arabica, C. canephora e derivados de Híbrido de Timor e Icatu cultivados nas principais regiões produtoras do Brasil. Após amplificação seletiva usando quatro combinações de primers (EcoRI/MseI), 100 fragmentos polimórficos foram analisados. Cada isolado apresentou um padrão único de alelos AFLP, demonstrando alta diversidade genotípica. A similaridade genética entre os isolados do patógeno variou de 0,08 a 0,70 e nenhuma formação de grupos foi observada no dendrograma. Não houve correlação entre similaridade genética e distância geográfica entre os isolados (r = 0,307, P = 0,234). Os isolados de H. vastatrix foram agrupados com base no hospedeiro em três populações (C. arabica, C. canephora e derivados de Híbrido de Timor/Icatu) e observou-se baixa diferenciação genética (GST = 0,026) entre elas. Após analisar as populações subdivididas com base na região geográfica a diversidade gênica (HT, HS e GST) não variou significativamente entre as populações e com base na AMOVA verificou-se que a variância genética (99,56%) ocorre dentro da população de H. vastatrix. A análise do número de migrantes (Nm) revelou alta taxa de fluxo gênico entre as populações originadas de hospedeiros distintos. Com base no índice de associação, a hipótese de acasalamento aleatório não foi rejeitada (IA = 0,22, P = 0,12) para a população do fungo proveniente de C. canephora. Os resultados apresentados demonstram que a população de H. vastatrix não possui uma estrutura populacional clonal, indicando um alto potencial evolutivo, o que traria implicações diretas no manejo deste patossistema, principalmente na obtenção de variedade com resistência durável.
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37

Lopes, Ester Souza. "Sequenciamento e caracterização de fragmentos de DNA de Brucella abortus gerados po SE-AFLP." reponame:Biblioteca Digital de Teses e Dissertações da UFRGS, 2010. http://hdl.handle.net/10183/70184.

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Espécies de Brucella são causadoras da brucelose, uma das doenças zoonóticas mais difundidas em todo o mundo, que é causa aborto em animais domésticos e infecção potencialmente debilitante em humanos. Apesar da identificação de diferentes espécies dentro do gênero, baseada na diferença de hospedeiro e patogenicidade, o gênero tem sido descrito como geneticamente homogêneo. Técnicas moleculares têm sido empregadas com o intuito de diferenciar e tipificar estes microrganismos, sendo que a abordagem mais promissora visa a identificação de polimorfismos entre as espécies e biovares. O objetivo do trabalho foi analisar o perfil genético de diferentes cepas de B. abortus obtidos a partir da técnica de SE-AFLP a fim de determinar a sequência dos fragmentos obtidos e genes que poderiam estar presentes nos fragmentos selecionados e compará-las com bancos de genes e de proteínas de procariotos. Foram selecionados 19 fragmentos, que foram purificados, sequenciados e, as sequências obtidas, submetidas a diversas ferramentas de bioinformática visando sua caracterização e identificação. Nenhum dos fragmentos de nucleotídeos apresentou similaridade entre si e/ou com outra sequência já conhecida de outros microrganismos, inclusive com sequências conhecidas do gênero Brucella. Das 114 proteínas hipotéticas geradas pela tradução destas sequências genômicas 57% (65 sequências) apresentaram baixo grau de similaridade com proteínas descritas e disponíveis em BLASTp (proteínas não-redundantes e SwissProt), variando entre 29 e 43. Do total de proteínas similares 85% foram atribuídas e proteínas funcionais e 14% a proteínas hipotéticas. Essas novas sequências deverão ser utilizadas em outros trabalhos visando verificar sua abrangência e especificidade dentro das espécies e biovares de Brucella.
Brucella species are the cause of brucellosis, one of the most widespread zoonotic diseases around the world, which is cause abortion in domestic animals and potentially debilitating infection in humans. Despite the identification of different species within the genus, based on the difference of host and pathogenicity, the genre has been described as genetically homogeneous. Molecular techniques have been employed in order to differentiate and classify these organisms, and the most promising approach aims to identify polymorphisms between species and biovars. The objective of this study was to analyze the genetic profile of different strains of B. abortus obtained by the technique of SE-AFLP to determine the sequence of the fragments obtained and genes that may be present in the selected fragments and compare them to databases of genes and proteins in prokaryotes. We selected 19 fragments that were purified, sequenced and the sequences obtained, subject to several bioinformatics tools aiming at its characterization and identification. None of the fragments showed nucleotide similarity between themselves and / or other sequence already known from other organisms, including known sequences of the genus Brucella. Of the 114 hypothetical proteins generated by translation of genomic sequences 57% (65 sequences) showed low level of similarity to proteins described and available in blastp (protein non-redundant and SwissProt), ranging between 29 and 43. Of the proteins similar 85% were attributed to functional proteins and 14% to hypothetical proteins. These new sequences should be used in other studies to verify its completeness and specificity within the species and biovars of Brucella.
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38

Sarvela, Erika Renee. "DIFFERENTIATING BETWEEN INVASIVE AND NATIVE POPULATIONS OF BIGHEAD AND SILVER CARP USING MS-AFLP." OpenSIUC, 2020. https://opensiuc.lib.siu.edu/theses/2807.

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When a species is introduced outside their native range, the genetic diversity of the introduced population is generally decreased due to the founder effect, and the fitness of individuals in the introduced population may decrease due to inbreeding depression. Invasive species are a paradox to this paradigm because while the initial population size of an invasive species may be small in their non-native range, the individuals are able to survive, eat, and reproduce so successfully, that they have deleterious effects on native species. One mechanism that invasive species use to overcome a lack of genetic diversity and adapt to their new environment is CpG methylation, a heritable and environmentally influenced epigenetic modification that regulates the expression of certain genes to alter phenotypes without altering an organism’s DNA sequence.Bighead and silver carps, two species of bigheaded carp native to eastern Asia, are believed to have been introduced to the United States in the 1970s. Since that time, populations of both bighead and silver carp have surged, particularly in the Mississippi River drainage, where they compete with native planktivores for food, injure boaters, and threaten the multi-million dollar fisheries industry in the Great Lakes. In this study, methylation-sensitive amplified fragment length polymorphisms (MS-AFLPs) were used to analyze the genetic and epigenetic diversity of bighead and silver carp from the Gan, Pearl, and Yangtze rivers in their native China and from the Illinois River in the United States. While the heterozygosity of silver carp in Illinois was not found to be significantly lower than that of silver carp in China, the silver carp in Illinois did show a significantly higher level of methylation compared to Chinese silver carp. There is evidence that CpG methylation may play a significant role in allowing silver carp to adapt and thrive in an introduced environment.
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39

Potter, Maria Louise. "AFLP fingerprint analysis of hybrid salamanders in the Missouri Caverns section of Onondaga Cave." Diss., Rolla, Mo. : Missouri University of Science and Technology, 2008. http://scholarsmine.mst.edu/thesis/pdf/Potter_Maria_09007dcc80679a5b.pdf.

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Thesis (M.S.)--Missouri University of Science and Technology, 2008.
Vita. The entire thesis text is included in file. Title from title screen of thesis/dissertation PDF file (viewed June 9, 2009) Includes bibliographical references (p. 107-111).
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40

Larsson, Josefine. "Population genetic structure and connectivity of the abundant sea urchin, Diadema setosum around Unguja island (Zanzibar)." Thesis, Södertörns högskola, Institutionen för livsvetenskaper, 2009. http://urn.kb.se/resolve?urn=urn:nbn:se:sh:diva-2824.

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The distribution and abundance of many coral reef organisms are affected by their predator’s distribution and abundance. Loss of predators may cause a shift in species compositions that will cascade down to other ecological processes on the reef. One example of a shift like this is the growing sea urchin populations inhabiting the coral reefs of East Africa. Areas with high fishing pressure often have large populations of sea urchins. The large populations of sea urchins have a negative impact on the reef ecology both by their grazing and bio-erosion as well as on fish growth and the recovery of fish populations. Previous population genetic studies conducted on Diadema setsosum, using mtDNA and allozymes, found genetic structuring between populations on a large geographical and evolutionary scale. The aim of this study was to examine the genetic population structure of the sea urchin Diadema setosum, at four sites around Zanzibar. We used the amplified fragment length polymorphism (AFLP) technique, a fast and effective method with high resolution. The long term objective is to understand the migration pattern and colonization of D. setosum to facilitate possible management actions. We found a significant genetic structuring of D. setosum hence the populations can not be considered panmictic. The reason behind this structure does not seem to be based on the geography nor size. One possible explanation might be that the structure lies on a larger geographical scale than we have studied, further studies around the Western Indian Ocean may reveal this. Another explanation may be that the structuring is due to differences in spawning time between the different phenotypes and an analysis of gonad maturations may give information about this. To find the reasons behind the observed genetic structure is of great importance for management of the sea urchins and therefore the management of whole reef ecosystems.
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41

Kabbage, Mehdi. "Amplified fragment length polymorphism in Mycosphaerella graminicola." Diss., Manhattan, Kan. : Kansas State University, 2007. http://hdl.handle.net/2097/255.

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42

Motta, Lucimar Barbosa da. "Aspectos químicos e moleculares ligados à filogenia de Camarea (Malpighiaceae)." Universidade de São Paulo, 2007. http://www.teses.usp.br/teses/disponiveis/41/41132/tde-05112007-112440/.

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Camarea St.-Hil. (Malpighiaceae) é um gênero endêmico da América do Sul, constituído por nove espécies. O objetivo do trabalho foi a reconstrução da filogenia do gênero, por meio de evidências químicas e moleculares. Foram avaliados nove terminais, sete dos quais são espécies correntemente reconhecidas, um é uma espécie que entrou em sinonímia (C. triphylla = C. axillaris) e outro é um suposto híbrido. Como grupos externos, foram utilizadas as espécies Peixotoa reticulata e Janusia guaranitica. Foram analisados os n-alcanos das ceras epicuticulares e os flavonóides de todas as espécies. Os n-alcanos principais foram C29, C31 e C33, todos da série normal. Como flavonóides característicos de Camarea, foram identificados glicosídeos de apigenina, luteolina, crisoeriol, campferol e quercetina. A análise de agrupamentos baseada na distribuição de alcanos, usando UPGMA e distâncias euclideanas, resultou em dois grupos principais, um com C29 como homólogo principal, constituído por C. hirsuta, C. affinis x C. hirsuta, C. affinis e C. ericoides. O outro grupo caracteriza-se por homólogos principais C31 ou C33, e é formado por C. elongata, C. humifusa, C. sericea, C. axillaris e C. triphylla (= C. axillaris). Esses dois principais agrupamentos contêm grupos internos menores. Uma análise de UPGMA usando coeficiente de DICE e baseada na distribuição de agliconas de flavonóides forneceu um dendrograma com alguns agrupamentos coerentes com as afinidades reveladas pela distribuição de alcanos, como as associações: 1) C. hirsuta, C. affinis e C. affinis x hirsuta; 2) C. elongata e C. axillaris; 3) C. sericea e C. humifusa. Uma inferência filogenética molecular foi obtida com seqüências de duas regiões do cloroplasto (trnL-F e rps16) e uma nuclear (ITS). Dentre as análises com um só marcador, resultados mais consistentes foram conseguidos com ITS, que forneceu 49 caracteres filogeneticamente informativos, enquanto trnL-F e rps16 forneceram 10 e 18 caracteres informativos, respectivamente. A análise de consenso estrito de quatro árvores mais parcimoniosas de uma análise combinando-se as três seqüências resultou em um cladograma em que Camarea é um grupo monofilético, com \"bootstrap\" (BS) 100, várias politomias e clados com baixa consistência. Foi realizada análise por AFLP utilizando quatro combinações de iniciadores seletivos, obtendo-se 217 fragmentos polimórficos. Uma análise combinando as evidências moleculares resultantes de seqüências de DNA e marcadores AFLP forneceu uma única árvore mais parcimoniosa com uma politomia agrupando C. affinis, C. ericoides, C. hirsuta e C. affinis x C. hirsuta, mas boa resolução e elevada sustentação em outros clados. A combinação de todas as evidências moleculares e químicas (estas compreendendo três caracteres derivados da análise de alcanos e cinco de flavonóides) resultou numa única árvore mais parcimoniosa completamente resolvida. Os resultados apóiam a fusão de C. triphylla em sinonímia com C. axillaris e indicam forte associação entre: 1) C. humifusa e C. sericea (BS 94); 2) C. affinis, C. affinis x hirsuta, C. hirsuta e C. ericoides (BS 83); 3) C. axillaris e C. elongata (BS 100). C. affinis, C. hirsuta e C. affinis x C. hirsuta compartilham a presença crisoeriol. C. affinis e C. affinis x C. hirsuta, compartilham também luteolina e formam um clado com BS 70. O presente trabalho demonstra a utilidade de caracteres químicos para melhorar a resolução de filogenias e elevar a sustentação de clados.
Camarea St.-Hil. (Malpighiaceae) is a genus with eight species endemic in South America. The purpose of the present work was the attainment of a phylogenetic inference of the genus by means of chemical and molecular evidences. Nine accessions were analyzed: seven correspond to currently recognized species; one is a species sunk into synonymy (C. triphylla = C. axillaris); and a last one is a hypothesized hybrid. Peixotoa reticulata and Janusia guaranitica were used as out-groups. n-Alkanes from epicuticular waxes and flavonoids were analyzed from all species. The main alkanes of all distributions were either C29 or C31 or C33, all from the normal series. The characteristic flavonoids of Camarea were shown to be apigenin, luteolin, chrysoeriol, kaempferol and quercetin. A cluster analysis based on the alkane distribution using UPGMA and Euclidean distances provided two main clusters. One cluster is characterized by C29 as main homologue and is formed by C. hirsuta, C. affinis, C. affinis x hirsuta and C. ericoides. The other cluster has species with either C31 or C33 as main homologue and is formed by C. elongata, C. humifusa, C. sericea, C. axillaris and C. triphylla (= C. axillaris). These two main clusters contain smaller inner clusters. An analysis using UPGMA and DICE coefficients and based on the distribution of flavonoid aglycones provided a dendrogram with clusters congruent with affinities revealed by the alkane evidence, such as the groupings: 1) C. hirsuta, C. affinis and C. affinis x hirsuta; 2) C. elongata and C. axillaris; 3) C. sericea and C. humifusa. A phylogenetic molecular inference was obtained with sequences from two chloroplast (trnL-F and rps16) and one nuclear (ITS) DNA regions. Among the analyses based on a single marker, more consistent results were obtained with ITS, which provided 49 informative phylogenetic characters, while trnL-F and rps16 provided 10 and 18 informative characters, respectively. A strict consensus analysis based on four more parsimonious trees from an analysis combining sequences of the three DNA regions gave a cladogram showing Camarea as a monophyletic group with bootstrap support (BS) 100. The cladogram contains several polytomies and clades with low support. An AFLP analysis, using four combinations of selective primers, provided 217 polymorphic fragments. Data from sequencing and AFLP were combined in a phylogenetic analysis. A sole more parsimonious tree was obtained, with most clades completely resolved with and high support. A polytomy remained, grouping C. affinis, C. ericoides, C. hirsuta and C. affinis x hirsuta. The combination of all molecular and chemical evidences (the latter comprising three alkane and five flavonoid characters) was used for a phylogenetic analysis. A sole more parsimonious tree was obtained, completely resolved and with clades highly supported. The results support sinking C. triphylla into synonymy of C. axillaris and indicate strong kinship: 1) between C. humifusa and C. sericea (BS 94); 2) among C. affinis, C. affinis x C. hirsuta, C. hirsuta and C. ericoides (BS 83); 3) between C. axillaris and C. elongata (BS 100). C. affinis, C. hirsuta and C. affinis x C. hirsuta share the possession of chrysoeriol. C. affinis and C. affinis x C. hirsuta share the possession also of luteolin and form a clade with BS 70. The present work reveals the utility of chemical characters to improve resolution of phylogenies and increment clade support.
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43

Pattanaik, Swapnendu. "Distribution, diversity and relationships in Dendrocalamus hamiltonii Munro : an appraisal using GIS and AFLP markers." Thesis, Bangor University, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.445098.

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44

Van, Staden Derick. "AFLP and PCR markers for the Ht1, Ht2, Ht3 and Htn1 resistance genes in maize." Thesis, Stellenbosch : Stellenbosch University, 2001. http://hdl.handle.net/10019.1/52078.

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Thesis (PhDAgric)--University of Stellenbosch, 2001.
ENGLISH ABSTRACT: Maize is undoubtedly South Africa's most important field crop. The identification of markers and genes for traits of interest is important to sustain the improvement of maize cultivation. Northern corn leaf blight (NClB) is a disease that occurs worldwide and can dramatically reduce yield. A number of single dominant resistance genes have been identified for NClB and some have been mapped. Currently there are no simple PCR markers for any of these resistance genes, making markerassisted selection (MAS) difficult. The aim of this study was to develop PCR markers for the NClB resistance genes Ht1, Ht2, Ht3 and Htn1 in maize. To accomplish this, the AFlP (amplified fragment length polymorphism) technique was first optimised. The results indicated that the Mlul/Msel restriction enzyme combination produces a higher percentage of polymorph isms when compared to the PstllMsel enzyme combination. It was also shown that the enzyme combination plays an important role in the percentage of polymorphic fragments observed, whereas the number of restriction enzymes used in AFlP analysis only significantly affects the total number of fragments scored. Populations segregating for the different resistance genes were not available for this study. Nearly-isogenic lines (Nils) were used in combination with AFlP technology to identify markers that map close to the genes. AFlP markers common in at least two resistant or susceptible lines were cloned and converted to PCR markers. Two commercially available recombinant inbred line (Ril) populations were then used to map the identified markers. For Htn1 fifteen polymorphic fragments were present in both resistant lines. They were selected for sequence specific marker conversion. Seven of the fifteen sequence characterized amplified region (SCAR) markers were polymorphic on the Nil pairs and five mapped to one region of maize chromosome 8.05/06. Twenty-one AFlP markers were identified for Ht1 and four SCAR markers were polymorphic In the Ht1 Nils. Three of these were mapped to chromosome 2.07. Three AFlP markers were identified for Ht2 of which two were converted to SCAR markers. Both SCAR markers were polymorphic on the Ht2 Nils and mapped to chromosome 8.05/06. On the Ht3 NILs, four AFLP markers were identified and two converted SCAR markers and one microsatellite marker (bnlg1666) were polymorphic. One of the SCAR markers and the microsatellite marker were mapped to chromosome 7.04 using a RIL population. This reports the first tentative mapping position for the Ht3 locus. The next step was to determine if a set of marker alleles could be used in a number of Htn 1 resistance lines to identify a common donor region selected by the breeders. Nine markers consisting of five SCAR markers, three converted RFLP markers and one microsatellite marker were used on 16 Htn1 resistant lines. The marker allele of us3 was in 12 of the 16 lines in coupling with Htn1 resistance. Second was the marker us5 in 11 of the 16 lines. Using this data 14 of the 16 lines shared a common introgressed region between the markers us3 and us5. A further common introgressed region between 11 of the inbred lines was found between the markers us14 and asg17. The last aim of this study was to propose a new marker technique that might be more successful than the AFLP technique in the identification of markers closely linked to genes. A new marker approach was identified where a MITE (Hbr) primer was used as an anchor primer in combination with resistance gene analog primers. This was found to be a highly polymorphic marker technique that could be used to identify markers and possibly candidate genes. It is a robust technique, which is affordable since amplifications occur from undigested genomic DNA and the primers mainly amplify fragments from genic regions.
AFRIKAANSE OPSOMMING: Mielies (Zea mays) is ongetwyfeld Suid Afrika se belangrikste lanbou gewas. Vir volgehoue opbrengs verbetering is die identifisering van merkers en gene vir belangrike eienskappe noodsaaklik. Noordelike blaarskroei (NBS) kan opbrengs wesenlik kan beïnvloed. Tans is daar reeds "n aantal enkel weerstandsgene geïdentifiseer, maar geen PKR-merkers is beskikbaar vir merker gebaseerde seleksie nie. Die doelwit van hierdie studie was om PKR-merkers te ontwikkel vir vier enkel weerstands gene (Ht1, Ht2, Ht3 en Htn1) teen NBS in mielies. Om die doelstelling te bereik is die AFLP-tegniek eers geoptimiseer. Op grond van waargenome aantal polimorfismes, was Mlul/Mse/"n beter restriksie ensiem kombinasie as Pstl/Msel. In die studie is ook bewys dat die aantal (meer as twee) restriksie ensieme wat gebruik word slegs die aantal fragmente, en nie die persentasie polimorfismes, wesenlik beïnvloed nie. Geen segregerende populasie was vir die verskillende gene beskikbaar nie. Naby isogeniese lyne (NILe) is daarom in kombinasie met die AFLP-tegniek gebruik om merkers te identifiseer wat naby die gene karteer. Alleenlik polimorfiese merkers wat in ten minste twee weerstand biedende of vatbare lyne voorgekom het, is gekloneer en omgeskakel na PKR-merkers. Daarna is twee kommersiële rekombinante ingeteelde lyn populasies gebruik om die gene te karteer. Vyftien fragmente is gevind wat gekoppel was met die Htn1 weerstand. Sewe van hierdie merkers is omgeskakel in polimorfiese SCAR-merkers waarvan vyf gekarteer is in een gebied op chromosoom 8.05/06. Een-en-twintig AFLP-merkers is geïndentifiseer vir Ht1 en vier is omgeskakel na polimorfiese SCAR-merkers. Drie hiervan is gekarteer op chromosoom 2.07. Drie AFLP-merkers is geïndetifiseer vir Ht2 waarvan 2 omgeskakel is na polimorfiese SCAR-merkers. Altwee hierdie merkers is gekarteer op chromosoom 8.05/06. Op die Ht3 lyne is vier AFLP-merkers geïdentifiseer waarvan twee omgeskakel is na polimorfiese SCAR-merkers. Een mikrosatelliet merker (bnlg1666) is ook gevind wat die selfde polimorfiese patroon wys op die Ht3 lyne. Die mikrosateliet en een van die SCAR-merkers het gekarteer op chromosomale posisie 7.04. Hierdie is die eerste tentatiewe posisie vir die Ht3 lokus. Die volgende stap was om te bepaal of "n stel polimorfiese merker-allele gebruik kan word om die donor DNA-segment te identifiseer wat die plantteiers geselekteer het. Nege PKR-merkers wat bestaan het uit vyf SCAR-merkers, 3 omgeskakelde RFLP merkers en een mikrosateliet is gebruik op 16 Hnt1 weerstandslyne. Us3 was die merker alleel wat in die meeste gevalle gekoppel was met die Htn1 weerstandslyne (12/16). Tweede was die merker us5 (in 11 van die 16 lyne). Uit die data blyk dit dat 14 van die 16 lyne "n donor segment het wat beide merkers us3 en us5 bevat. Merkers us14 en asg17 het in 11 van die 16 bestande lyne saam voorgekom. Die laaste doelstelling van hierdie studie was om "n nuwe tegniek te ontwikkel wat dalk meer suksesvol as AFLPs kan wees om merkers te identifiseer nabyaan gene. "n Nuwe tegniek word voorgestel waar "n MITE (Hbr) inleier gebruik kan word in kombinasie met weerstandgeen-analoog inleiers. Dit is gevind dat hierdie kombinasie van inleiers "n hoogs polimorfiese band patroon gee en dat die merkers ook dalk kandidaat-gene kan wees. Die tegniek is maklik uitvoerbaar, relatief goedkoop en maak gebruik van onverteerde genomiese DNA. Die fragmente wat geamplifiseer word is hoofsaaklik vanaf geenryke areas.
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45

Lopes, Francisco Claudio da Conceição. "Mapeamento genético de cana-de-açúcar (Saccharum spp.) por associação empregando marcadores SSR e AFLP." Universidade de São Paulo, 2011. http://www.teses.usp.br/teses/disponiveis/11/11137/tde-29062011-152130/.

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A cultura da cana-de-açúcar (Saccharum spp.) possui uma importância histórica e econômica para o Brasil. O agronegócio sucroalcooleiro vem experimentando forte expansão na última década não só no Brasil como também em todo o mundo em função, principalmente, da demanda por fontes de energia menos agressivas ao ambiente. Para atender a uma maior demanda por seus subprodutos, principalmente de etanol, a área cultivada com cana-de-açúcar vem aumentando a cada ano no Brasil, ocupando áreas novas de cultivo nas regiões centrais do país. Nesse contexto, o melhoramento genético tem um papel fundamental no desenvolvimento de novas cultivares adaptadas a essas condições de cultivo. A maioria dos caracteres de importância econômica possui uma natureza genética complexa fazendo com que o desenvolvimento de uma nova cultivar de cana-de-açúcar leve mais de 10 anos. Desta forma, o uso de abordagens que permitam a identificação de genes ou de QTLs associados a caracteres quantitativos de forma precisa e rápida tem grande utilidade no melhoramento dessa espécie. O mapeamento por associação baseado no fenômeno do desequilíbrio de ligação é uma metodologia que visa detectar associações entre genes e caracteres agronômicos, podendo contribuir desta forma para o melhoramento da cana-de-açúcar. Assim, este trabalho teve como principal objetivo avaliar o uso da abordagem de mapeamento por associação na detecção de associações importantes entre marcadores moleculares do tipo SSR e AFLP e os caracteres Altura, Diâmetro e Número de Colmos; Percentual de Fibra na Cana (Fibra % Cana); Porcentagem em massa de sacarose (Pol % cana) e Tonelada de Cana por Hectare (TCH) em cana-de-açúcar. Os dados fenotípicos dos genótipos avaliados são oriundos de experimentos conduzidos em quatro regiões: Ribeirão Preto, Jaú e Piracicaba em São Paulo e Goianésia em Goiás no período entre 1990 e 2009. Associações entre os marcadores e os caracteres fenotípicos foram avaliadas em cada região e em todas simultaneamente. A análise de associação realizada através de modelos mistos sugeriu a existência de doze associações envolvendo os caracteres Número de Colmos, Porcentagem em massa de sacarose (Pol % cana) e Tonelada de Cana por Hectare (TCH). Quatro associações envolveram a característica Número de Colmos sendo três (CIR56, ACG_CGT e AGG_CAG) de caráter geral, ou seja, relacionada à média das quatro regiões e uma associação na região de Goiás (ACG_CAT). Sete associações entre a característica Pol % Cana e as marcas CV60, CV106, AAG_CAC, AAG_CAG e ACG_CTT foram específicas para a região de cultivo de Ribeirão Preto. Uma associação entre Tonelada de Cana por Hectare (TCH) e a marca ACG_CGC foi detectada na região de Piracicaba.
Sugarcane (Saccharum spp.) has an historical and economic relevance in Brazil. We are the largest producer and exporter of sugar and ethanol in the world. Sugar agribusiness has experienced a xx in the last decade not only in Brazil but also around the world as a consequence of increasing demand on renewable and clean sources of energy. As a consequence, the growing area with sugarcane in Brazil is expanding, reaching the central regions of the country. Sugarcane breeding has an important role in developing new cultivars adapted to these new conditions. However, most traits of economic importance in sugarcane have complex genetic architecture making the improvement of new sugarcane cultivars a challenging process. Thus, adoption of strategies that allow for rapid and precise detection of genes associated with quantitative traits is of great interest, representing a valuable tool for sugarcane breeding. Association mapping based on linkage disequilibrium represents a strategy useful for detection of marker-trait associations and may contribute for identifying genes useful for sugarcane breeding. In the present study, association mapping approach was applied to sugarcane in order to evaluate its potential contribution in detecting important associations between SSR and AFLP molecular markers and the characters Height, Diameter and Number of Stalks; % Fiber; % Pol and TCH. Phenotypic data for genotypes were collected from field trials in four locations: Ribeirão Preto, Jaú and Piracicaba in São Paulo and Goianésia in Goiás between 1993 and 2009. Marker-trait associations were tested for each location individually and for all locations simultaneously. A mixed model approach was adopted to test for marker-trait associations. The results suggested the existence of twelve associations involving the characters Stalk Number, % Pol and TCH. Four associations involved stalk number from which three (markers CIR56, ACG_CGT e AGG_CAG) were for all locations and one specific to Goiás (ACG_CAT). Seven associations between % Pol and markers CV60, CV106, AAG_CAC, AAG_CAG e ACG_CTT were detected in Ribeirão Preto. One association between TCH and ACG_CGC was detected in Piracicaba
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46

Tsuji, Koji. "Original birthplace of cultivated Tartary buckwheat(Fagopyrum tataricum Gaertn.)revealed by RAPD and AFLP markers." Kyoto University, 2001. http://hdl.handle.net/2433/150759.

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Kyoto University (京都大学)
0048
新制・課程博士
博士(農学)
甲第8987号
農博第1169号
新制||農||819(附属図書館)
学位論文||H13||N3506(農学部図書室)
UT51-2001-F317
京都大学大学院農学研究科応用生物科学専攻
(主査)教授 大西 近江, 教授 遠藤 隆, 教授 谷坂 隆俊
学位規則第4条第1項該当
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47

Redondo, Mariana Letícia Costa. "Caracterização molecular por AFLP (Amplified Fragment Length Polymorphism) de acessos de pinhão manso (Jatropha curcas L.)." Universidade de São Paulo, 2011. http://www.teses.usp.br/teses/disponiveis/64/64133/tde-03102011-094124/.

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O pinhão-manso (Jatropha curcas L.) é uma planta versátil e com diversos usos potenciais em especial para produção de biodiesel. O óleo obtido de suas sementes é seu produto mais rentável e atualmente desperta grande interesse econômico em diversos setores. A caracterização molecular e a avaliação do potencial reprodutivo dos acessos de pinhão-manso são aspectos ainda pouco abordados no Brasil, sendo necessária a caracterização de acessos brasileiros e suas potencialidades. Os objetivos do presente trabalho foram analisar a diversidade genética e a divergência genética em acessos comerciais de pinhão-manso, coletados no estado de São Paulo (Alvinlândia, Lins, Itatinga e Jales), Minas Gerais (Janaúba) e Mato Grosso do Sul (Dourados). Primeiramente, foram comparadas as técnicas de RAPD (Random Amplified Polymorphic DNA), RAPD-RFLP (Restrinction Fragment Length Polymorphism a partir do RAPD) e AFLP (Amplified Fragment Length Polymorphism), quanto à potencialidade de detectar polimorfismos dentro dos acessos e entre os acessos. Posteriormente, os acessos foram caracterizados através de AFLP. Além disso, este trabalho visou detectar se há diferença nas estruturas e no desenvolvimento floral e na taxa de viabilidade polínica dos acessos de São Paulo (Alvinlândia), Minas Gerais e Mato Grosso do Sul. Nessa parte do estudo, foram analisadas e identificadas as estruturas dos órgãos florais e do grão de pólen através das técnicas de microscopia de luz, eletrônica de varredura e transmissão. Na comparação entre as técnicas moleculares, apenas AFLP permitiu a detecção de polimorfismos, com base em um acesso escolhido para os testes (Alvinlândia, SP). As análises de todos acessos através de AFLP mostraram considerável polimorfismo, que foi refletido nas estimativas de diversidade genética de Nei e Índice de Shannon. Na análise de agrupamento, as amostras de cada acesso foram agrupadas coerentemente. Os acessos de Dourados e de Itatinga formaram um grupo separado, apresentando cerca de 76% de similaridade com o segundo grupo (Alvinlândia, Jales, Lins, Janaúba). Dentro deste último, os acessos de São Paulo ficaram agrupados (com cerca de 84% de similaridade), enquanto que Janaúba mostrou-se separado, com 82% de similaridade genética. Estes resultados indicam que os acessos de São Paulo provavelmente tenham origem a partir de Janaúba. No entanto, Itatinga provavelmente tenha origem a partir de Dourados. Quanto à morfologia floral, não foi observada nenhuma diferença a nível microscópico na formação e nas estruturas dos órgãos florais. Quando comparada a viabilidade polínica entre os dois acessos coletados em campo (Minas Gerais e Mato Grosso do Sul), notou-se que há diferença significativa na taxa de viabilidade, mesmo os valores sendo muito próximos (Mato Grosso do Sul - 81,91% e Minas Gerais - 77,20%), mostra que tanto os acessos de Minas Gerais como os de Mato Grosso do Sul podem ser utilizados como parentais masculinos em programas de melhoramento genético. A divergência genética moderada e a baixa variabilidade morfológica sugerem que coletas de materiais em poucos locais poderiam representar a diversidade genética da espécie. Estudos mais aprofundados, empregando técnicas como de microssatélites e mais acessos, são 11 necessários para o conhecimento da diversidade e estrutura genética do pinhão-manso no Brasil
Physic nut (Jatropha curcas L) is a very versatile plant with several potential uses especially for the production of biodiesel. The oil obtained from its seeds is the most profitable product of this specie and it is currently attracting great interest in various economic sectors. Molecular characterization and evaluation of reproductive potential of the accessions of pysic nut have still little attention in Brazil, it still need the characterization of Brazilian accessions and its potenciality. The ains of this study were: to analyze the genetic diversity and genetic divergence in commercial accessions of physic nut, from the States of São Paulo (Alvinlândia, Lins, Jales and Itatinga), Minas Gerais (Janaúba)and Mato Grosso do Sul (Dourados). Firstly we compared the RAPD (Random Amplified Polymorphic DNA) RAPD-RFLP (Fragment Length Polymorphism Restriction from RAPD) and AFLP (Amplified Fragment Length Polymprphism) regarding the potencial to detect polymorphism within the accessions and among accessions. Subsequently, the accessions were characterized by AFLP. Moreover this work aimed to detect whether there are differenced on flower structures and development and the rate of pollen viability on the accessions of São Paulo (Alvinlândia), Minas Gerias and Mato Grosso do Sul. On this part of the study were analysed and identified the structures of the floral organs and pollen grain through the techniques of, light microscopy, scanning electron and transmission microscopy. Comparing the molecular techniques, only AFLP allowed the detection of polymorphisms based on the accession chosen for testing (Alvinlândia, SP). Analyses of all accesses by AFLP showed considerable polymorphism, wich was reflected in estimates of genetic diversity index of Nei and Shannon. In cluster analysis, samples of each accessions were grouped consistently. The accessions of Dourados and Itatinga formed a separated group, with approximately 76% similarity with the second group (Alvinlândia, Jales, Lins, Janaúba). Within the last, accessions of São Paulo werte grouped (about 84% similarity), while Janaúba showed p separately, with 82% of genetic similarity. These results indicates that the accessions of São Paulo probably originates from Janaúba. However Itatinga probably originates from Dourados. As floral morphology, we observed no difference at microscope level on the formation and on the structures of floral organs. When compared the pollen grain viability between the two accessions collected in the field (Minas Gerais and Mato Grosso do Sul), it was noted that the viability rated were significantly different, even though the values being very close (Mato Grosso do Sul Minas Gerais 81,91% - 77,20%), shows that both the accessions of Minas Gerais as the Mato Grosso do Sul can be used as male parental in breeding programs. The moderate and low genetic divergence suggests that morphological variability collections of materials in a few locations could represent the genetis diversity of the species. Further studies employing techniques such as microsatellite and more accessions are required for an understanding of diversity and genetic structure of physic nut in Brazil
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48

Kovach, Katherine Elizabeth. "Assessment of Genetic Variation of Acer rubrum L. and Liriodendron tulipifera L. Populations in Unmanaged Forests of the Southeast United States." Thesis, Virginia Tech, 2008. http://hdl.handle.net/10919/31282.

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Acer rubrum L. and Liriodendron tulipifera L. are prolific throughout their ranges in the Southeastern U.S. and also have increasingly important roles in forestry and wood products in this region. The relatively low density and intermediate strength of the wood makes them versatile for use in many different wood products. Exploring the genetic structure of these species could provide a foundation for further genetic and breeding exploration with these economically important trees. This study utilizes amplified fragment length polymorphism to determine the level of genetic diversity of these species in contrasting physiographic provinces. AFLP was performed using five primer combinations on samples collected from six unmanaged populations of each species in the Mountains and Coastal Plain of the Southeastern U.S. Wood density was determined using an X-ray densitometer. A. rubrum lacked strong genetic structure while L. tulipifera showed differentiation between physiographic provinces. Genetic diversity of A. rubrum was lower within the Mountain populations (He: 0.327) than the Coastal Plain populations (He: 0.365). The average wood density for A. rubrum is lower in the Mountains (539.00 kg/m^3) than in the Coastal Plain (575.43 kg/m^3). Genetic diversity of L. tulipifera was higher overall (He: 0.289) than within the Mountain populations (He: 0.281) or the Coastal Plain populations (He: 0.271). The average wood density for L. tulipifera is greater in the Mountains (445.45 kg/m^3) than in the Coastal Plain (441.67 kg/m^3).
Master of Science
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49

Jiménez, Arias Ana Patricia. "Genotipificación de Mycobacterium tuberculosis complex mediante herramientas moleculares." Doctoral thesis, Universitat Politècnica de València, 2016. http://hdl.handle.net/10251/62681.

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[EN] In the last years, various genotyping techniques were developed for isolation of Mycobacterium tuberculosis complex (MTBC) that has demonstrated a high discriminatory power. In this study, after the identification of selected strains at level of species by Genotype MTBC technique, we evaluated the profit of the simplified amplified-fragment Length Polymorphism technique (AFLPs) and the Mycobacterial Interspersed Repetitive Units technique (MIRU-15). A total of 131 mycobacterium tuberculosis isolates were analyzed, 68 isolates were collected in Ecuador, from the Clinical Laboratory of Hospital Alli Causai located in city of Ambato, and the Laboratory of Bacteriology in Carlos Andrade Marín Hospital located in the capital city Quito. The remaining 63 isolates were harvested in Spain and belong to microorganism's collection of Microbiology Services of Consorcio Hospital General Universitario and Hospital Clínico Universitario of the city of Valencia. Among these isolates, 126 were identified by conventional methods such as molecular MTBC, corresponding to 106 patients. The Mycobacterium tuberculosis control strain ATCC 25177 was also identified as such by this method. The AFLPs technique allowed as to group the strains in twelve patterns (P1 to P8, P10, P12, P13, P14), of which the most prevalent were patterns P1 with 77 (61.1%) and P2 with 27 (21, 4%) isolates, representing 82.5% of the same. These were followed by the pattern P5 with 5 (3.9%) isolates, the patterns P3, P4 and P6 grouped 3 isolates each one (2.4%), the patterns P8 and P12 with 2 isolates (1.6% ) and finally the patterns P7, P10, P13 and P14 with 1 isolated each one (0.8%). The control strain M. tuberculosis ATCC 25177, showed a restriction profile that prevented their inclusion in any of the patterns described. The discriminatory power of the Hunter-Gaston discriminatory index (HGDI) method was 0.5812 against to 0.9843 of the MIRU-15 technique, which grouped 69 strains (54.8%) in 20 clonal complex and 57 unique patterns (45.2%). In the case of Spain, the strains were related mostly to the lineage 4 or Euro-American including: Cammeroon (1.59%), Haarlem (36.51%), S (31.75%), and LAM (19.05%); the lineage 6 or West Africa I (9.53%), the lineage 1 or EIA (1.59%) In the case of Ecuador the strains were related to the lineage 4: Haarlem (42.86%), S (33.33%) and LAM (22.22%) and Beijing lineage 2 (1.59%) from Asia. The MIRU-VNTR Variable-Number Tandem Repeats (15 loci) technique proved to be a stable system, reproducible and high discriminatory power in comparison with AFLPs system, allowing the use of it to conduct prospective population studies with the aim of contributing to the public health programs to control Tuberculosis (TB).
[ES] En los últimos años se han desarrollado diversas técnicas de genotipificación para aislados de Mycobacterium tuberculosis complex (MTBC) que han demostrado tener un alto poder discriminatorio. En este estudio, tras identificación de las cepas seleccionadas al nivel de especie mediante la técnica comercial GenoType MTBC, se ha evaluado la utilidad de la técnica simplificada del Polimorfismo de Longitud de Fragmentos Amplificados (AFLPs) y la técnica de Unidades Repetitivas Intercaladas Micobacterianas (MIRU-15). Se analizaron un total de 131 aislados clínicos de los cuales 68 aislados fueron recolectados en Ecuador, provenientes tanto del Laboratorio Clínico del Hospital Alli Causai ubicado en la ciudad de Ambato, provincia de Tungurahua como del Laboratorio de Bacteriología del Hospital Carlos Andrade Marín ubicado en la ciudad capital Quito, provincia de Pichincha. Los 63 aislados restantes fueron recolectados en España y pertenecían colección de microorganismos de los Servicios de Microbiología del Consorcio Hospital General Universitario y Hospital Clínico Universitario de la ciudad de Valencia, provincia de Valencia. De éstos aislados, 126 fueron identificados por métodos convencionales y moleculares como MTBC, correspondientes a 106 pacientes. La cepa control Mycobacterium tuberculosis ATCC 25177 también fue identificada como tal mediante este método. La técnica AFLPs permitió agrupar a las cepas en doce patrones (P1 a P8, P10, P12, P13, P14), de los cuales los más prevalentes fueron los patrones P1 y P2 con 77 (61,1%) y 27 (21,4%) aislados respectivamente, lo que supone el 82,5% del total de los mismos. Le siguieron en frecuencia el patrón P5 con 5 (3,9%) aislados, los patrones P3, P4 y P6 agruparon a 3 aislados cada uno (2,4%), los patrones P8 y P12 con 2 aislados (1,6%) y finalmente los patrones P7, P10, P13 y P14 con 1 aislado cada uno (0,8%). La cepa control M. tuberculosis ATCC 25177, mostró un perfil de restricción que no permitió su inclusión en ninguno de los patrones descritos. El poder discriminatorio del método (HGDI) fue de 0,5812 frente a 0.9843 de la técnica MIRU-15, que agrupó a 69 cepas (54,8%) en 20 complejos clonales y 57 patrones únicos (45,2%). Para el caso de España, las cepas estuvieron relacionadas en su mayoría con el linaje 4 o Euro-Americano que incluye: Cammeroon (1,59%), Haarlem (36,51%), S (31,75%), y LAM (19,05%); el linaje 6 o West Africa I (9,53%), el linaje 1 o EIA (1,59%), Para el caso de Ecuador las cepas estaban relacionadas con el linaje 4: Haarlem (42,86%), S (33,33%), y LAM (22,22%) y el linaje 2 Beijing (1,59%) originario de Asia. La técnica MIRU-VNTR (15 loci) demostró ser un sistema estable, reproducible y con un poder discriminatorio alto en comparación con AFLPs lo que permitiría emplearlo para realizar estudios poblacionales prospectivos con la finalidad de contribuir a los programas de Salud Pública para el control de la Tuberculosis (TB).
[CAT] En els últims anys s'han desenvolupat diverses tècniques de genotipificació per aïllats de Mycobacterium tuberculosis complex (MTBC) que han demostrat tenir un alt poder discriminatori. En aquest estudi, després de la identificació de les soques seleccionades al nivell d'espècie mitjançant la tècnica comercial GenoType MTBC, s'ha avaluat la utilitat de la tècnica simplificada del Polimorfisme de longitud de fragments amplificats (AFLPs) i la tècnica d'Unitats repetitives Intercalades micobacterianes (Miru-15). Es van analitzar un total de 131 aïllats clínics dels quals 68 aïllats van ser recollectats a Equador, provinents tant del Laboratori Clínic de l'Hospital Alli Causai situat a la ciutat d'Ambato, província de Tungurahua com del Laboratori de Bacteriologia de l'Hospital Carlos Andrade Marín ubicat a la ciutat cabdal Quito, província de Pichincha. Els 63 aïllats restants van ser recollectats a Espanya i pertanyien a la collecció de microorganismes dels Serveis de Microbiologia del Consorci Hospital General Universitari i Hospital Clínic Universitari de la ciutat de València, província de València. D'aquests aïllats, 126 van ser identificats per mètodes convencionals i moleculars com MTBC, corresponents a 106 pacients. La soca control Mycobacterium tuberculosi ATCC 25177 també va ser identificada com a tal mitjançant aquest mètode. La tècnica AFLPs va permetre agrupar les soques en dotze patrons (P1 a P8, P10, P12, P13, P14), dels quals els més prevalents van ser els patrons P1 i P2 amb 77 (61,1%) i 27 (21, 4%) aïllats respectivament, fet que suposa el 82,5% del total dels mateixos. El van seguir en freqüència el patró P5 amb 5 (3,9%) aïllats, els patrons P3, P4 i P6 van agrupar a 3 aïllats cadascun (2,4%), els patrons P8 i P12 amb 2 aïllats (1,6%) i finalment els patrons P7, P10, P13 i P14 amb 1 aïllat cadascun (0,8%). La soca control M. tuberculosis ATCC 25177, va mostrar un perfil de restricció que no va permetre la seva inclusió en cap dels patrons descrits. El poder discriminatori del mètode (HGDI) va ser de 0,5812 enfront de 0,9843 de la tècnica MIRU-15, que va agrupar a 69 soques (54,8%) en 20 complexos clonals i 57 patrons únics (45,2%). Per al cas d'Espanya, les soques van estar relacionades majoritàriament amb el llinatge 4 o Euro-Americà que inclou: Cammeroon (1,59%), Haarlem (36,51%), S (31,75%), i LAM (19,05%); el llinatge 6 o West Africa I (9,53%), el llinatge 1 o EIA (1,59%), Pel cas de l'Equador les soques estaven relacionades amb el llinatge 4: Haarlem (42,86%), S ( 33,33%), i LAM (22,22%) i el llinatge 2 Beijing (1,59%) originari d'Àsia. La tècnica Miru-VNTR (15 loci) va demostrar ser un sistema estable, reproduïble i amb un poder discriminatori alt en comparació amb AFLPs, el que permetria emprar-lo per realitzar estudis poblacionals prospectius amb la finalitat de contribuir als programes de salut pública per al control de la Tuberculosi (TB).
Jiménez Arias, AP. (2016). Genotipificación de Mycobacterium tuberculosis complex mediante herramientas moleculares [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/62681
TESIS
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50

Saito, Suzane. "Caracterização in silico de sequências polimórficas na população de Sporisorium scitamineum e análise da expressão de genes vizinhos aos polimorfismos." Universidade de São Paulo, 2015. http://www.teses.usp.br/teses/disponiveis/11/11137/tde-20102015-155648/.

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O fungo Sporisorium scitamineum é o agente causador de uma das doenças mais importantes da cultura da cana-de-açúcar, o carvão da cana, e vem sendo alvo de diversos estudos genéticos para a elucidação de seu mecanismo de patogenicidade e interação com o seu hospedeiro. Dentre esses estudos há os que visam acessar a variabilidade genética entre isolados desse fungo utilizando diversos marcadores moleculares, porém todos os experimentos indicaram baixa variabilidade, com exceção de isolados provenientes da Ásia. O primeiro estudo realizado com esse intuito em isolados brasileiros utilizou o tel-RFLP e AFLP, obtendo uma variabilidade de 34 e 3%, respectivamente. O AFLP é muito utilizado para a detecção de variação genética em indivíduos próximos, porém, nesse caso, apresentou baixa variação, o que nos levou a caracterizar, no presente trabalho, os poucos polimorfismos encontrados através dessa técnica. Os fragmentos polimórficos foram reamplificados, sequenciados e caracterizados quanto ao seu contexto genômico. Como essas sequências estão dispersas ao longo do genoma e geralmente estão em regiões intergênicas, foi feita a análise de expressão dos genes vizinhos a esses polimorfismos em três condições distintas. Desses genes, 70% apresentaram maior número de reads mapeadas in planta que em meio de cultura, indicando que são mais importantes durante a interação planta-patógeno. Dessa forma, mesmo havendo uma baixa variabilidade detectada por AFLP, essas diferenças podem ser importantes na regulação desses genes, podendo influenciar na agressividade do patógeno e na sua defesa.
The fungi Sporisorium scitamineum is the causal agent of one of the most important diseases in sugarcane, the sugarcane smut, and it has been the target of several genetic studies aiming the elucidation of pathogenicity and host interaction macanisms. Among these studies are those that aim to access the genetic variability among isolates of this fungus using various molecular markers techniques, however in all of them the experiments indicated low variability, with exception of the Asian isolates. The first work performed with Brazilian isolates was done using tel-RFLP and AFLP, and detected a variability of 34 and 3%, respectively. The AFLP is widely used to detect variability in close related individuals, but in this case, the method revealed low polimorphism. These results led us to characterize in the present work the few polymorphisms detected. The polymorphic fragments were isoladed, reamplified, sequenced and in silico characterized regarding the genomic context. Since these sequences are disperse along the genome and generally they are in intergenic regions, an expression analysis of the polymorfisms neighbor genes was made at three different conditions. Of these genes, 70% presented higher numbers of maped reads in planta than in culture media, which indicates that they are important during the plant-pathogen interaction. Thus, even with low variability detected via AFLP, these differences can be important in the gene regulation and may influence in the pathogen agressivity and in its defense.
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