The aim of this study was to obtain the molecular marker of Taiwania cryptomerioides Hayata based on DNA sequence data of PCR- sequencing and inter-simple sequence repeat (ISSR), and to evaluate the genetic diversity of populations of Taiwania cryptomerioides Hayata and molecular phylogeny of T. cryptomerioides and Taiwania flousiana Gaussen. The sequence data based on the internal transcribed spacer (ITS) of a total of 108 samples of T. cryptomerioides were determined. Eight different populations of T. cryptomerioides and 12 samples of T. flousiana from Yunnan, China were analyzed. The finding of the study showed that heterogeneity of ITS region within individuals of T. cryptomerioides was high by showing high nucleotide diversity among ITS sequences both in T. cryptomerioides ( £k = 0.18153) and T. flousiana ( £k = 0.19751). The findings fit in Tajima¡¦s D test of neutrality based on DNA sequence variation in the ITS region of T. cryptomerioides and T. flousiana. It is not obvious to incorporate into different population through clustering analysis based on data of the ITS region of T. cryptomerioides and T. flousiana. However, slightly genetic differentiation between T. cryptomerioides and T. flousiana was found, which figured of Fst (Fst = 0.0441~ 0.0856, an average value = 0.0611). On the other hand, the samples were studied by using ISSR markers. Of the 100 primers screened, 4 produced highly reproducible ISSR bands, and 24 discernible DNA fragments were generated with 17 being polymorphic. Based on cluster analysis of molecular data, the cluster is not clear among populations of T. cryptomerioides and T. flousiana. The analysis of AMOVA revealed that the variance component between species of T. cryptomerioides and T. flousiana was 38.54¢H (P < 0.001); however, the variance component within species is 61.46 (P < 0.001). The variation within population of T. cryptomerioides was 84.74¢H (P < 0.001) and the variance between populations is 15.26¢H (P < 0.001), indicating that the genetic diversity of individuals within population was high. The aforementioned data suggest that gene flow among different populations of T. cryptomerioides was high, indicating that the genetic diversity was high among individuals of T. cryptomerioides but was low between populations. Furthermore, it is concluded both species are genetically closer and could be grouped into the same species.

The objective of this study is to elucidate the efficiency of enation-structure (at node) recognition method at pre-flowing stage and to understand the population genetic variation of the Mikania weeds in Taiwan. The plant materials collected by recognizing enation-structure symptom method from North, Central, South and East Taiwan and off-shore islands. Using PCR¡V sequencing marker techniques, the sequencing revealed that nrDNA ITS region could identify three Mikania weeds and the 97% similarity of phylogenetic relationship between M.cordata and M.micrantha are more closer than that between M.cordata and M.scandens, whose ITS sequence is obtained from GeneBank. However ,the sequences of chloroplast DNA of M.cordata and M.micrantha at trnL intron¡]436bp¡^or trnL-trnF IGS¡]345 bp¡^are almost the same and could not be used as molecular markers. The recognizing techniques of enation-structure was supported by the nrDNA ITS region and ISSR results at the end, thus the finding can be recommended to the Council of Agriculture in order to eliminate the weed and to reduce the impact on M.cordata, which is native in Taiwan. Moreover, the findings of ISSR analysis in the aspect of population genetic variation indicated that high genetic differentiation ¡]Gst>0.5¡^was found among the M. cordata and M.micrantha populations. Based on the Mantle test, there was no relationship between genetic distance and geographic distance in M.micrantha¡]r=0.0053,p=0.47¡^.This phenomenon revealed that populations of M.micrantha had complex population variability within the short-term invaded into Taiwan that might be resulted from the random dispersion of human activities. The population of M.micrantha was established by few individuals (founders) and grown rapidly in Taiwan, resulting in population differentiation via genetic drift. In contrast to M.micrantha ,there was relationship between genetic distance and geographic distance in M.cordata ¡]r=0.44,p=0.025¡¯¡^.It revealed that populations of M.cordata agreed to the concept of isolation by distance model, which might be evolved from the result of natural dispersion. In conclusion, the population structure of M.micrantha in Taiwan is stable , suggesting that control of Mikania population should be based on different populations where have large differentiation among them .

Several oomycete species of the genus Saprolegnia are recognized as devastating fish pathogens and are responsible for the loss of millions of fish annually for the aquaculture industry. Until recently, these pathogens were kept in check using malachite green; however, due to its toxicity, this chemical has now been banned from use. Saprolegnia parasitica is recognized as the major pathogen of aquaculture fish species. The industry is struggling to predict and control S. parasitica outbreaks in fish hatcheries and there is a need for new knowledge regarding the population genetic structure of this pathogen. Random amplified microsatellites were used to compare isolates of S. parasitica collected from a variety of hatchery locations during the period of November 2009 - August 2011, in order to determine the level of genetic variability and determine changes in genetic diversity over time. Allele frequencies of scored characters were graphically compared. Population genetic diversity was measured using Nei’s genetic distance, Shannon’s Information Index, number of polymorphic loci and phylogenetic trees. Due to the presence of Saprolegnia parasitica in the facilities tested, it appears to be ubiquitous in aquaculture facilities and treatment and prevention will be an ongoing concern in aquaculture management. Overall, genetic diversity of S. parasitica isolates was determined to be low with at least some sexual recombination occurring over time. There was a diversity of genotypes collected from the same hatchery on a single day, indicating there was not a single genotype present at a given time point. Genetic profiling, such as used here, could provide facility managers with a new approach to develop a series of best practices to control sporadic outbreaks of disease. Use of these genetic markers and close monitoring of S. parasitica genotypes will permit early detection and sanitation protocols. / Graduate / 2015-04-24 / 0476 / 0792 / 0369 / cren06@uvic.ca

Submitted by Amanda Silva (amanda.osilva2@ufpe.br) on 2015-04-08T12:53:20Z No. of bitstreams: 2 Dissertação Nathália Leite.pdf: 1163803 bytes, checksum: ed3fcb6e6b34f0c3e3452518a29c3263 (MD5) license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) / Made available in DSpace on 2015-04-08T12:53:20Z (GMT). No. of bitstreams: 2 Dissertação Nathália Leite.pdf: 1163803 bytes, checksum: ed3fcb6e6b34f0c3e3452518a29c3263 (MD5) license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) Previous issue date: 2012-02-29 / CNPq / O presente estudo foi realizado com os objetivos de identificar acessos de feijão-caupi tolerantes ao caruncho (C. maculatus) e caracterizar esses acessos a nível molecular, em conjunto a acessos de V. unguiculata ssp. cylindrica e V. radiata, por meio de marcadores DAF (DNA Amplification Fingerprinting) e ISSR (Inter Simple Sequence Repeat), visando identificar parentais promissores para futuros trabalhos de melhoramento, bem como para mapeamento, pela associação com o nível de resposta ao caruncho. Para identificação da tolerância ao caruncho em feijão-caupi, 27 acessos foram avaliados em ensaios de laboratório, utilizando-se o Delineamento Experimental Inteiramente Casualizado. Para cada acesso, uma amostra com 30 grãos de feijão-caupi foi infestada com cinco casais de caruncho com até 24 h de idade, sendo os resultados obtidos submetidos à análise estatística e suas médias comparadas pelo teste de Tukey a 5% de probabilidade. Para as duas variáveis estudadas, o acesso INHUMA comportou-se como suscetível, enquanto os acessos PATATIVA e MNC99-537F-4 apresentaram-se tolerantes para ambas as variáveis. Os demais acessos testados apresentaram comportamento intermediário, o que não os diferencia em relação à INHUMA, PATATIVA e MNC99-537F-4. Na caracterização molecular dos acessos, 25 primers geraram um total de 239 amplicons, dos quais 163 foram polimórficos. Os fragmentos amplificados foram incluídos em uma matriz de dados para análise pelo método de Neighbor-Joining. No fenograma obtido, V. radiata e V. unguiculata ssp. cylindrica assumiram uma posição basal isolada dos subgrupos formados, enquanto que os acessos de V. unguiculata subdividiram-se em dois grupos, nos quais os acessos contrastantes quanto à tolerância ao caruncho se distribuíram em subgrupos distintos, o que evidencia a existência de diferenças genéticas significativas entre alguns candidatos. Nesse sentido, os resultados obtidos demonstraram que os ensaios de tolerância ao caruncho associados à aplicação de marcadores moleculares foram capazes de identificar genótipos contrastantes de feijão-caupi promissores para aplicação em trabalhos de melhoramento vegetal, bem como para a geração de populações segregantes adequadas ao mapeamento genético.

Phytophthora sojae, the causal organism of stem and root rot, and <i>Soybean mosaic virus</i> (SMV) cause two of the most highly destructive diseases of soybean (<i>Glycine max</i> L. Merr). <i>P. sojae</i> can be managed either through deployment of race-specific resistance or through quantitative resistance termed partial resistance. In the current study, partial resistance to <i>P. sojae</i> was mapped in an interspecific recombinant inbred line (RIL) population of <i>Glycine max</i> by <i>Glycine soja</i>. One major quantitative trait loci (QTL) on molecular linkage group (MLG)-J (chromosome 16) and two minor QTL on MLG-I (chromosome 20) and -G (chromosome 18) were mapped using conventional molecular markers. Additionally, partial resistance to <i>P. sojae</i> was mapped in the same RIL population using single feature polymorphism (SFP) markers that further fine mapped the <i>P. sojae</i> QTL and identified potential candidate genes contributing to resistance. In a separate study, race-specific resistance was characterized in PI96983 discovering a potentially new allele of <i>Rps4</i> on MLG-G. Finally, using the newly available whole-genome shotgun sequence of soybean, <i>Rsv4</i> conferring resistance to strains of SMV known in the US, was localized to an approximately 100 kb region of sequence on chromosome 2 (MLG-D1B). Newly designed PCR-based markers permit for efficient selection of <i>Rsv4</i> by breeding programs. Identified candidate genes for <i>Rsv4</i> are discussed. Genomic resources developed in all of these studies provide breeders the tools necessary for developing durable resistance to both SMV and <i>P. sojae</i>. / Ph. D.

No description available.

Previously seed coat color in flax has been used as a phenotypic marker for specialty quality traits and currently there is an increasing demand to use seed coat color in flax to market flax for human and animal nutrition uses. Seed coat color was studied to 1) understand the inheritance of seed coat color conditioned by the b1 locus, to 2) understand the relationship of other important flax traits with seed coat color as well as to 3) identify markers that are linked to seed coat color for future marker assisted selection of seed coat color. Spearman’s rank correlation and an allelism test was used to show the inheritance of the alleles at the b1 locus. Bulked segregant analysis (BSA) was used to identify putatively linked markers with the b1 locus, these were then screened on the CDC Bethune x M96006 recombinant inbred line population. Furthermore, the CDC Bethune x M96006 and CDC Bethune x USDA-ARS Crystal recombinant inbred line populations were used to identify any important flax traits that had a significant relationship with seed coat color. It was shown that seed coat color conditioned by the b1 locus was stably inherited and that b1vg and b1 are allelic to one another. The results of the BSA showed that there were 17 candidates for linkage but when these markers were screened on the population only the Lu456 from linkage group (LG) six was identified to have linkage (χ²=3.90; P<0.05) with the b1 locus. Additionally, it was shown that the b1 seed coat color allele of the b1 locus had a pleiotropic effect on flower color and flower shape and that seed coat color was associated with linolenic fatty acid content. None of the traits examined were found to be associated with the b1vg allele of this locus. These results show that the b1 locus is likely present on linkage group six, more marker coverage on linkage group six of markers that are polymorphic between the two seed coat color parents would increase the accuracy of detection. Lastly, this study showed that plant breeders should consider using the b1vg allele that conditions the variegated seed coat color to mark unique lines with important combinations of traits because it sorted independently for seed quality traits. Whereas, the yellow seed coat color conditioned by the b1 allele was found to be associated with higher linolenic fatty acid content and the semi-lethality of this allele would make it not suitable for use in parental lines.

In this study, strawberry fruit was taken as the studied model. An attempt was carried on trying to identify a unique DNA fingerprint in each of the selected different strawberry cultivars of Fragaria x ananassa Duch species available in Turkey. The basis of the study was to examine the fruit characteristics at the molecular level rather than at the morphological level. It is of great importance to differentiate and trace the origin of any variety by examining its DNA by using a very sophisticated molecular technique. In this case, DNA fingerprinting technique depending on the Simple Sequence Repeats (SSRs) markers which are also called Microsatellite markers were used. DNA fingerprinting technique reveals the specific DNA profile which is unique as a fingerprint for a fruit specimen and this DNA profile is the same and constant throughout different parts of the fruit as well as its developmental stages. In this thesis work, nine primers flanking the SSR markers already available in the online databases were designed hoping to detect SSRs that could differentiate among the five selected cultivars of strawberry.

Made available in DSpace on 2014-08-20T13:25:42Z (GMT). No. of bitstreams: 1 Tese_Luciano_Carlos_da_Maia.pdf: 871025 bytes, checksum: fcb02e5ff38b9223264b40df7fe04318 (MD5) Previous issue date: 2009-07-03 / Molecular markers have been successfuly applied in genetic mapping and marker assisted selection as an auxiliary tool for plant breeding and transfer of genetic information among related species. In this sense, the understanding of genome elements occurring in important crop species such as wheat, rice and maize can be used towards the improvement of basic knowledge in orphan grass species. Rice, after the completion of its genome sequence, has been proposed as a genetic model in the grasses. Among the different types of molecular markers, microsatellites have been indicated as the preferred class for such studies. In general, the strategy of transposing molecular markers between species still poses some questions/difficulties regarding the most conserved microsatellite patterns among plant species, genera and families. This study had as objective to use bioinformatic tools to characterize microsatellites from rice and other Grass species of economical importance, enabling the prediction of microsatellite patterns that are most promising in transfer strategies. Three studies were performed. The first was concerned about developping and validating a microsatellite searching tool plus primer design and PCR simulation. A database containing 28,469 fl-cDNA sequences originating from japonica rice genome was used. From a total of 3,907 microsatellite loci, 3,329 primer pairs were designed and tested using the simulated PCR feature showing that only 2,397 (72%) of pairs amplified in specific regions. The second study had as objective to describe the occurrence of microsatellites in expressed regions originating from ten species from three different plant families. The results indicated the frequency and patterns of occurrence of microsatellites within and between the different families. The third study had as objective to characterize the complete occurrence of microsatellites in the rice genome. The results showed a different pattern of occurrence of microsatellites for the different chromosomes and which arrangements are most abundant. Inferences on which elements allow better genome coverages are discussed. / Marcadores moleculares têm sido utilizados com sucesso em mapeamento genético e seleção assistida como uma ferramenta auxiliar para o melhoramento de plantas e transferência de informações entre espécies relacionadas. Neste sentido, o entendimento da ocorrência de microssatélites no genoma nas diferentes espécies melhoradas como trigo, arroz e milho pode ser utilizado no sentido da melhoria do conhecimento básico das espécies gramíneas descritas como “orfãs”. O arroz, após a conclusão do seqüênciamento do seu genoma, tem sido proposto como modelo genético entre as gramíneas. Dentre os diferentes tipos de marcadores moleculares, os microssatélites são indicados como a classe preferida para estes estudos. De maneira geral, as estratégias de transposição de marcadores moleculares entre espécies ainda apresentam algumas dificuldades e questionamentos referentes os padrões mais conservados de microssatélites entre espécies, genêro e famílias vegetais. Este estudo teve como objetivo, o uso de ferramentas de bioinformática para caracterizar microssatélites oriundos do genoma do arroz e outras espécies, possibilitando predizer padrões de microssatélites mais promissores na transferência. Três estudos foram realizados. O primeiro consistiu no desenvolvimento e validação de uma ferramenta para localização de microssatélites, desenho de iniciadores e simulação da PCR. Foi utilizado um banco de dados contendo 28.469 seqüências fl-cDNA de arroz japonica. Do total de 3.907 loci encontrados, foram desenhados 3.329 conjuntos de iniciadores e testados pela simulação da PCR, mostrando que somente 2.397 (72%) iniciadores amplificaram regiões específicas. No segundo estudo foi analisada a ocorrência de microssatélites em regiões expressas de dez espécies de três diferentes famílias de plantas. Os resultados indicaram a freqüência e padrões de microssatélites dentro e entre as diferentes famílias. No terceiro estudo foi feita a caracterização de microssatélites no genoma completo do arroz. Os resultados mostraram um conservado padrão de ocorrência dos diferentes microssatélites nos diferentes cromossomos e quais os arranjos foram os mais abundantes. Inferências sobre quais elementos permitem a melhor cobertura do genoma foram discutidas.

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / Aceria guerreronis keifer is one of the main coconut pests in Brazil, its attack causes a premature fall, reduction of fruit size, water weight and volume, as well as stetic esthetic damages (necrosis) depreciating the product. Currently, there are five pesticides registered for the control of the coconut-necrotic mite. However, there is no specificity to A. guerreronis. The Lamiaceae family stands out with some specimens with notable insecticidal activity, among them the Vitex genus, known to have ecdysteroids and iridoids as markers of the genus. However, there is a shortage of specific chemotaxonomic studies for volatile compounds. The objective of this work was to identify the volatile compounds present in the essential oils of the species of Vitex gardneriana Schauer, Vitex capitata Vahl., Vitex rufescens A. Juss., Vitex megapotamica (Spreng.) Moldenk and to evaluate possible effects of toxicity and repellence against A. guerreronis. In addition to analyzing the genetic diversity of species of the genus Vitex using ISSR markers, verifying the occurrence of statistical correlations between the genetic diversity and the chemical profiles of the essential oils. Chromatographic and spectroscopic techniques (GC-MS / FID) were used for the detection of volatile compounds, and the molecular markers of ISSR for the genetic characterization of the species, as well as toxicity and repellency tests against necrotic necrosis. The results showed 46, 45, 41 and 37 constituents for V. capitata, V. megapotamica, V. gardneriana and V. rufences respectively, among which, -copaene, (E)-caryophyllene, -elemene, -humulene, trans-cadine-1(6)4-diene, viridiflorene and -cadinene were the main components of V. capitata and V. megapotamica. 6,9-guaiadiene, caryophyllene oxide, L-calamenene for V. gardneriana and (E)-cariophylene, ledol, germacrene D, -humulene, allo-aromadendrene, viridiflorene and -elemene for V. rufences. The results of molecular markers of ISSR generated a total of 90 fragments, of which 100% were polymorphic. The genotypes of the four Vitex species selected for this study were pooled using the Jaccard coefficient (JC). The mean similarity was 0.21 JC (0.08-0.45 JC). A clear separation of two groups was observed, with V. gardneriana being the most isolated of the four species, and V. capitata and V. megapotamica more closely related to each other. The acaricide activity of the four oils was also evaluated by means of toxicity and repellency tests against A. guerreronis. The essential oil of V. gardneriana showed acaricidal activity against A. guerreronis with a LC50 of 0.85 mg.mL-1, whereas the oils of V. capitata, V. megapotamica and V. rufecens were not toxic to this pest up to 2.3 mg. Ml-1 when tested through the toxicity bioassay. In general, essential oils distilled from the Vitex species repelled A. guerreronis after 24 hours at a concentration of 1.8 mg.mL-1 using abamectin as a control in the two-choice disc repellency assay, however, the essential oil of V. gardneriana presented a statistically significant acaricidal activity against the coconut mite necrosis. Introducing himself as a potential candidate for the development of an acaricide product. / O ácaro-da-necrose-de-coqueiro Aceria guerreronis keifer é uma das principais pragas de coqueiro do Brasil, seu ataque causa queda prematura, redução no tamanho e peso dos frutos e volume de água, além dos danos estéticos (necroses) na casca que diminui o valor comercial do produto. Atualmente, existem cinco agrotóxicos registrados para o controle dessa praga. No entanto, não há especificidade ao A. guerreronis. A família Lamiaceae se destaca com alguns exemplares com notória atividade inseticida, dentre eles, o gênero Vitex, conhecido por possuir dentre seus constituintes os ecdisteroides e iridoides como marcadores do gênero, todavia, há uma escassez de estudo quimiotaxonômicos específicos para compostos voláteis. O objetivo deste trabalho foi identificar os compostos voláteis presentes nos óleos essenciais das espécies de Vitex gardneriana Schauer, Vitex capitata Vahl., Vitex rufescens A. Juss., Vitex megapotamica (Spreng.) Moldenk e avaliar possíveis efeitos de toxicidade e repelência frente ao A. guerreronis, além de analisar a diversidade genética de espécies do gênero Vitex. Técnicas cromatográficas e espectroscópicas (CG-MS/FID) foram utilizadas para detecção dos compostos voláteis, e os marcadores moleculares de ISSR foram empregados para a caracterização genética das espécies, além de testes de toxicidade e repelência contra ao àcaro-da-necrose. Os resultados mostraram 46, 45, 41 e 37 constituintes para V. capitata, V. megapotamica, V. gardneriana e V. rufences respectivamente, dentre os quais, -copaeno, (E)-cariofileno, -elemeno, -humuleno, trans-cadina-1(6),4-dieno, viridiflorene e -cadineno foram os principais componentes de V. capitata e V. megapotamica. 6,9- guaiadieno, óxido de cariofileno, L-calameneno para V. gardneriana e (E)-cariofileno, ledol, germacreno D, -humuleno, allo-aromadendreno, viridifloreno e -elemene para V. rufences. Os resultados dos marcadores moleculares de ISSR geraram um total de 90 fragmentos, dos quais 100% foram polimórficos. Os genótipos das quatro espécies de Vitex selecionadas para este estudo foram agrupados utilizando o coeficiente Jaccard (JC). A média de similaridade foi de 0,21 JC (0,08-0,45 JC). Observou-se uma clara separação de dois grupos, sendo V. gardneriana a mais isolada das quatro espécies, e V. capitata e V. megapotamica mais próxima geneticamente entre si. A atividade acaricida dos quatro óleos também foi avaliada por meio de ensaios de toxicidade e repelência contra o àcaro-da-necrose. O óleo essencial de V. gardneriana mostrou atividade acaricida ao A. guerreronis com uma CL50 de 0,85 mg.mL-1, enquanto que os óleos de V. capitata, V. megapotamica e V. rufecens não foram tóxicos para esta praga até 2,3 mg.ml-1, quando testados através do bioensaio de toxicidade. Em geral, os óleos essenciais destilados a partir das espécies de Vitex repeliram o A. guerreronis após 24 horas a uma concentração de 1.8 mg.mL-1 utilizando abamectina como controle no ensaio de repelência disco de duas escolha, no entanto, o óleo essencial de V. gardneriana apresentou atividade acaricida estatisticamente significativa frente ao ácaro-da-necrose-do-coqueiro. Apresentando-se como potencial candidato para o desenvolvimento de um produto acaricida. / São Cristóvão, SE