Caracterización de Germoplasma sobresaliente de papa solanum tuberosum L. en México mediante RAPD y SSR

1Tesis ( Doctor en Ciencias con Especialidad en Biotecnología ) U.A.N.L.

Diversidade genética em duas populações de Pterogyne nitens Tul. utilizando SSR

Pós-graduação em Agronomia (Genética e Melhoramento de Plantas) - FCAV

Estrutura genética de populações de Crinipellis perniciosa e Moniliophthora roreri utilizando marcadores RAPD e SSR

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Molecular and Pathogenic Diversity Among Brazilian Isolates of Xanthomonas albilineans Assessed with SSR Marker Loci

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Diversidade genética em populações de Candidatus Liberibacter asiaticus determinada por marcadores SSR

Pós-graduação em Agronomia (Genética e Melhoramento de Plantas) - FCAV

Optimierung von Transformationsprotokollen und Entwicklung von SSR-Markern für das Kolumnarwachstum beim Apfel

Ziel war es, molekularbiologische Untersuchungen zum Kolumnarwachstum des Apfels durchzuführen. Anhand Sequenzdaten des ‘Golden Delicious’ Genoms (Velasco et al. 2010) wurden drei neue SSR Marker entwickelt. Sie konnten bei untersuchten Geisenheimer Nachkommenschaften zuverlässig den Kolumnarwuchs auf DNA-Ebene detektieren. Zusätzlich wurden von Bai et al. (2012) veröffentlichte Marker untersucht. Die von Bai et al. (2012) gefundenen Grenzen des co-Lokus konnten in dieser Arbeit anhand der Geisenheimer Nachkommenschaften nicht bestätigt werden. Die „linke“ Begrenzung der co-Region wird nach Untersuchungen dieser Arbeit am ehesten von dem Marker Mdo.chr10.11 (Moriya et al. 2012) bei 18,757 Mbp definiert. Die „rechte“ Begrenzung der co-Region wird vermutlich von den Markern Co04R13 (Baldi et al. 2012) und C1753-3520 (Bai et al. 2012) bei 18,905 Mbp definiert, wodurch die potentielle co-Region auf 148 kb auf Chromosom 10 eingegrenzt werden könnte. Für Funktionsanalysen möglicher Kandidatengene des co-Gens wurde ein Agrobakterien-vermitteltes Transformationssystem für die Geisenheimer Apfelselektionen ‘A 14’ und ‘Procats 28’ adaptiert. Zusätzlich wurde der bereits in der Literatur als transformierbar beschriebene Genotyp ‘Jonagold’ (Viss et al. 2003) transformiert. Bei Transformationen der Apfelselektion ‘A 14’ gelang es, transgene Zellen an den Explantaten, am Kallusgewebe und an den Regeneraten zu erzeugen. Bei Transformationen von ‘Jonagold’ wurde ein fast vollständig transgenes Regenerat erzeugt.

Genetic diversity among alfalfa genotypes (Medicago sativa L.) of non-dormant cultivars using SSR markers and agronomic traits

The aim of this study was to assess genetic diversity among 40 alfalfa (Medicago sativa L.) genotypes of different non-dormant (FD=8) cultivars. Biomass yield, regrowth speed and reaction to spring black stem, lepto leaf spot, and rust were evaluated. Analyses of variances were performed using a mixed model to examine the agronomic variation among individuals. A principal component analysis on standardized agronomic data was performed. Agronomic data were also used to calculate Gower's distance and UPGMA algorithm. For the molecular analysis, six SSR markers were evaluated and 84 alleles were identified. The genetic distance was estimated using standard Nei's distance. Average standard genetic diversity was 0.843, indicating a high degree of variability among genotypes. Finally, a generalized procrustes analysis was performed to calculate the correlation between molecular and agronomic distance, indicating a 65.4% of consensus. This value is likely related to the low number of individuals included in the study, which might have underestimated the real phenotypic variability among genotypes. Despite the low number of individuals and SSR markers analyzed, this study provides a baseline for future diversity studies to identify genetically distant alfalfa individuals or cultivars.

Análisis de algoritmos para posicionamiento de aeronaves mediante respuestas SSR utilizando recepción omnidireccional

El transporte aéreo constituye un sector estratégico para el crecimiento económico de cualquier país. El sistema de gestión de tráfico aéreo ATM tiene como objetivo el movimiento seguro y eficiente de las aeronaves dentro del espacio aéreo y de los aeropuertos, siendo la seguridad, en la fase táctica, gestionada por el servicio de control de la circulación aérea. Mediante los procesos de control el tráfico aéreo es vigilado a través de sensores, regulado y guiado de forma organizada y segura. Es precisamente sobre la vigilancia donde se enfoca el contenido de la tesis, en el desarrollo de nuevos conceptos que proporcionen información de vigilancia de ‘bajo coste’ basados en las señales existentes proporcionadas por la infraestructura actual de radar secundario y por los sistemas de posicionamiento basados en satélite que utiliza la ADS-B. El conocimiento y acceso en tiempo real a las trayectorias de las aeronaves es un elemento de valor añadido no sólo para la provisión de los servicios de control de tránsito aéreo, sino para todos los actores del transporte aéreo o de la investigación, siendo uno de los elementos clave en el concepto operacional de los dos grandes proyectos tecnológicos, SESAR en Europa y NextGen en EE.UU.. En las últimas décadas el control de la circulación aérea en espacios aéreos de media y alta densidad de tráfico se ha basado en tecnologías complejas que requieren importantes infraestructuras como son el radar primario de vigilancia (PSR) y el radar secundario de vigilancia (SSR). La filosofía de los programas SESAR y NextGen siguiendo las directrices de la OACI es la de alejarse de las tecnologías basadas en tierra para evolucionar hacia nuevas tecnologías más dinámicas basadas en satélite como la ADS-B. Pero hasta que la implementación y operación de la ADS-B sea completa, existirá un período de transición que implica la coexistencia de aeronaves equipadas o no con ADS-B. El objetivo de la presente Tesis es determinar las metodologías y algoritmos más adecuados para poder hibridar las dos tecnologías descritas anteriormente, utilizando para ello un receptor de bajo coste con antena estática omnidireccional, que analice todas las señales presentes en el canal que comparten el SSR y ADS-B. Mediante esta hibridación se podrá obtener la posición de cualquier aeronave que transmita respuestas a interrogaciones SSR, en cualquiera de sus modos de trabajo, o directamente mensajes de posición ADS-B. Para desarrollar los algoritmos propuestos, además del hardware correspondiente, se han utilizado las aplicaciones LabVIEW para funciones de adquisición de datos reales, y el software MATLAB® para el desarrollo de algoritmos y análisis de datos. La validación de resultados se ha realizado mediante los propios mensajes de posición ADS-B y a través de las trazas radar proporcionadas por la entidad pública empresarial ENAIRE. La técnica desarrollada es autónoma, y no ha requerido de ninguna otra entrada que no sea la recepción omnidireccional de las señales. Sin embargo para la validación de resultados se ha utilizado información pública de las ubicaciones de la red de estaciones SSR desplegadas sobre territorio español y portugués y trazas radar. Los resultados obtenidos demuestran, que con técnicas basadas en superficies de situación definidas por los tiempos de llegada de las respuestas, es posible determinar con una precisión aceptable la posición de las estaciones SSR y la posición de cualquier aeronave que responda mediante el Modo A a éstas. ABSTRACT Air transport is a strategic sector for the economic growth of any country. The air traffic management system (ATM) aims at the safe and efficient movement of aircraft while operating within the airspace and airports, where safety, in the tactical phase, is managed by the air traffic control services. Through the air traffic control processes, aircraft are monitored by sensors, regulated and guided in an organized and safe manner. It is precisely on surveillance where this thesis is focused, developing new concepts that provide a 'low cost' surveillance information based on existing signals provided by currently secondary radar infrastructure and satellite-based positioning systems used by ADS-B. Having a deeper knowledge and a real-time access to the trajectories of the aircraft, is an element of added value not only for the provision of air traffic control services, but also for all air transport or research actors. This is one of the key elements in the operational concept proposed by the two large scale existing technological projects, SESAR in Europe and NextGen in the US. In recent decades, air traffic control in medium and high traffic density areas has been based on complex technologies requiring major infrastructures, such as the primary surveillance radar (PSR) and secondary surveillance radar (SSR). The philosophy of SESAR and NextGen programs, both following the guidelines of ICAO, is to move away from land-based technologies and evolving into some new and more dynamic satellite-based technologies such as ADS-B. Nevertheless, until the ADS-B implementation and operation is fully achieved, there will be a transitional period where aircraft with and without ADS-B equipment will have to coexist. The main objective of this thesis is to determine those methodologies and algorithms which are considered more appropriate to hybridize those two technologies, by using a low cost omnidirectional receiver, which analyzes all signals on the SSR and ADS-B shared channel. Through this hybridization, it is possible to obtain the position of any aircraft answering the SSR interrogations, in any of its modes of operation, or through the emission of ADS-B messages. To develop the proposed algorithms, LabVIEW application has been used for real-time data acquisition, as well as MATLAB software for algorithm development and data analysis, together with the corresponding hardware. The validation of results was performed using the ADS-B position messages and radar tracks provided by the Public Corporate Entity ENAIRE The developed technique is autonomous, and it does not require any other input other than the omnidirectional signal reception. However, for the validation of results, not only radar records have been used, but also public information regarding the position of SSR stations spread throughout the Spanish and Portuguese territory. The results show that using techniques based in the definition of positioning surfaces defined by the responses’ times of arrival, it is possible to determine with an acceptable level of accuracy both the position of the SSR stations as well as the position of any aircraft which transmits Mode A responses.

Sequence-tagged microsatellite profiling (STMP): a rapid technique for developing SSR markers

We describe a technique, sequence-tagged microsatellite profiling (STMP), to rapidly generate large numbers of simple sequence repeat (SSR) markers from genomic or cDNA. This technique eliminates the need for library screening to identify SSR-containing clones and provides an ∼25-fold increase in sequencing throughput compared to traditional methods. STMP generates short but characteristic nucleotide sequence tags for fragments that are present within a pool of SSR amplicons. These tags are then ligated together to form concatemers for cloning and sequencing. The analysis of thousands of tags gives rise to a representational profile of the abundance and frequency of SSRs within the DNA pool, from which low copy sequences can be identified. As each tag contains sufficient nucleotide sequence for primer design, their conversion into PCR primers allows the amplification of corresponding full-length fragments from the pool of SSR amplicons. These fragments permit the full characterisation of a SSR locus and provide flanking sequence for the development of a microsatellite marker. Alternatively, sequence tag primers can be used to directly amplify corresponding SSR loci from genomic DNA, thereby reducing the cost of developing a microsatellite marker to the synthesis of just one sequence-specific primer. We demonstrate the utility of STMP by the development of SSR markers in bread wheat.

Targeted development of informative microsatellite (SSR) markers

We describe a novel approach, selectively amplified microsatellite (SAM) analysis, for the targeted development of informative simple sequence repeat (SSR) markers. A modified selectively amplified microsatellite polymorphic loci assay is used to generate multi-locus SSR fingerprints that provide a source of polymorphic DNA markers (SAMs) for use in genetic studies. These polymorphisms capture the repeat length variation associated with SSRs and allow their chromosomal location to be determined prior to the expense of isolating and characterising individual loci. SAMs can then be converted to locus-specific SSR markers with the design and synthesis of a single primer specific to the conserved region flanking the repeat. This approach offers a cost-efficient and rapid method for developing SSR markers for predetermined chromosomal locations and of potential informativeness. The high recovery rate of useful SSR markers makes this strategy a valuable tool for population and genetic mapping studies. The utility of SAM analysis was demonstrated by the development of SSR markers in bread wheat.

Rationalization of taro germplam collections in the Pacific Island region using simple sequence repeat (SSR) markers

A regional (Oceania) core collection for taro germplasm has been developed based on phenotypic and molecular characterization. In total, 2199 accessions of taro germplasm have been collected by TaroGen (Taro Genetic Resources: Conservation and Utilisation) from 10 countries in Oceania: Papua New Guinea, Solomon Islands, Vanuatu, New Caledonia, Fiji, Palau, Niue, Tonga, Cook Islands and Samoa. Our objective was to select 10% from each country to contribute to a regional core. The larger collections from Papua New Guinea, Vanuatu and New Caledonia were analysed based on phenotypic characters, and a diverse subset representing 20% of these collections was fingerprinted. A diverse 20% subsample was also taken from the Solomon Islands. All accessions from the other six countries were fingerprinted. In total, 515 accessions were genotyped (23.4% overall) using taro specific simple sequence repeat (SSR) markers. DNA fingerprint data showed that great allelic diversity existed in Papua New Guinea and the Solomon Islands. Interestingly, rare alleles were identified in taros from the Solomon Islands province of Choiseul which were not observed in any of the other collections. Overall, 211 accessions were recommended for inclusion in the final regional core collection based on the phenotypic and molecular characterization.

Current range characteristics of Swiss stone pine (Pinus cembra L.) along the Carpathians revealed by chloroplast SSR markers.

We investigated the diversity pattern of nine Swiss stone pine (Pinus cembra L.) populations along the Carpathian range including the High Tatras, by using six chloroplast DNA microsatellites (cpSSR). Our aim was to detect genetically distinct regions by clustering of populations, and to tackle possible historical colonization routes. Our analysis referred to an investigated geographical range with the two most distant populations situated at about 500 air km. We found that the most diverse populations are situated at the two edges of the investigated part, in the Retezat Mts. (South Carpathians) and the High Tatras, and diversity decreases towards the populations of the Eastern Carpathians. Hierarchical clustering and NMDS revealed that the populations of the South Carpathians with the Tatras form a distinct cluster, significantly separated from those of the Eastern Carpathians. Moreover, based on the most variable chloroplast microsatellites, the four populations of the two range edges are not significantly different. Our results, supported also by palynological and late glacial macrofossil evidences, indicate refugial territories within the Retezat Mts. that conserved rich haplotype composition. From this refugial territory Pinus cembra might have colonized the Eastern Carpathians, and this was accompanied by a gradual decrease in population diversity. Populations of the High Tatras might have had the same role in the colonizing events of the Carpathians, as positive correlation was detected among populations lying from each other at a distance of 280 km, the maximum distance between neighbouring populations.

Les technologies de l'information et de la télécommunication (TIC) pour la promotion de la santé sexuelle et reproductive (SSR) au sein des jeunes des Premières Nations du Québec : faisabilité et pistes d'intervention

La répartition des taux de prévalence des infections transmissibles sexuellement et par le sang (ITSS) et du VIH/SIDA au Canada présente de grandes inégalités entre les différents groupes socioculturels. Les Autochtones font partie des populations qui en payent le plus lourd tribut. Par rapport à cette situation, le plan directeur 2007-2017 de la commission de la santé et des services sociaux des Premières Nations du Québec et du Labrador (CSSSPNQL) identifie clairement le VIH/SIDA comme une problématique prioritaire de santé. La stratégie autochtone sur le VIH/SIDA estime que pour être efficaces, les interventions visant la prévention du VIH/SIDA doivent cibler divers groupes, au nombre desquels la jeunesse autochtone est une cible particulière. En ce sens, la familiarité des jeunes générations avec la technologie positionne l’utilisation des technologies de l’information et de la communication (TIC) comme une avenue fortement prometteuse dans le domaine de la prévention du VIH/SIDA chez les adolescents et jeunes adultes. Nous avons réalisé une synthèse des connaissances dans ce domaine novateur suivant une méthodologie suggérée par la Collaboration Cochrane dans le but de documenter l’efficacité et les facteurs d’adoption des interventions utilisant les TIC pour la prévention des ITSS/VIH/SIDA et la promotion de la santé sexuelle et reproductive auprès des adolescents et jeunes adultes. Les résultats de cette revue systématique ont permis d’élaborer et de mener, en partenariat avec la CSSSPNQL, un projet de recherche visant à évaluer la faisabilité de telles interventions au sein des adolescents et jeunes adultes de communautés des Premières Nations (PN) du Québec. En complément à cette étude de faisabilité et dans le but de formuler des recommandations en vue de la conception d’interventions utilisant les TIC et fondées autant sur les données probantes que sur les réalités des jeunes des PN, nous avons entrepris une dernière étude visant à identifier les facteurs sous-jacents du port du condom chez les 13-18 ans de communautés des Premières Nations du Québec. Nous avons discuté, dans la présente thèse, les résultats de ces études ainsi que divers enjeux du partenariat de recherche avec les parties prenantes des PN ayant participé à notre projet. Les implications pratiques de nos résultats, en matière de recherche et d’intervention, sont à discuter avec notre principale partenaire, la CSSSPNQL, afin d’en optimiser les retombées pour les populations des PN.