From a fresh data science perspective, this thesis discusses the prediction of coronary artery disease based on Single-Nucleotide Polymorphisms (SNPs) from the Ontario Heart Genomics Study (OHGS). First, the thesis explains the k-Nearest Neighbour (k-NN) and Random Forest learning algorithms, and includes a complete proof that k-NN is universally consistent in finite dimensional normed vector spaces. Second, the thesis introduces two dimensionality reduction techniques: Random Projections and a new method termed Mass Transportation Distance (MTD) Feature Selection. Then, this thesis compares the performance of Random Projections with k-NN against MTD Feature Selection and Random Forest for predicting artery disease. Results demonstrate that MTD Feature Selection with Random Forest is superior to Random Projections and k-NN. Random Forest is able to obtain an accuracy of 0.6660 and an area under the ROC curve of 0.8562 on the OHGS dataset, when 3335 SNPs are selected by MTD Feature Selection for classification. This area is considerably better than the previous high score of 0.608 obtained by Davies et al. in 2010 on the same dataset.

Advances in molecular methods for analyzing DNA, RNA and proteins in humans as well as in other animals, plants, fungi, bacteria or viruses have greatly increased the resolution with which we can study life’s complexity and dynamics on earth. While genomic, transcriptomic and proteomic laboratory tools for molecular diagnosis of disease are rapidly becoming more comprehensive, the access to such advanced yet often expensive and centralized procedures is limited. There is a great need for rapid and comprehensive diagnostic methods in low-resource settings or contexts where a person can not or will not go to a hospital or medical laboratory, yet where a clinical analysis is urgent. In this thesis, results from development and characterization of novel technologies for DNA and protein microarray analysis are presented. Emphasis is on methods that could provide rapid, cost-effective and portable analysis with convenient readout and retained diagnostic accuracy. The first study presents a magnetic bead-based approach for DNA microarray analysis for a rapid visual detection of single nucleotide polymorphisms. In the second work, magnetic beads were used as detection reagents for rapid differential detection of presence of pestiviral family members using a DNA oligonucleotide microarray with read-out by means of a tabletop scanner or a digital camera. In paper three, autoimmune responses from human sera were detected on a protein autoantigen microarray, again by means of magnetic bead analysis. Here, special emphasis was made in comprehensively comparing the performance of the magnetic bead detection to common fluorescence-based detection. In the fourth study, an immunochromatographic lateral flow protein microarray assay is presented for application in the classification of contagious pleuropneumonia from bovine serum samples. The analysis could be performed within 10 minutes using a table top scanner, and the performance of the assay was shown to be comparable to that of a cocktail ELISA. In the fifth paper, the lateral flow microarray framework is investigated in further detail by means of experiments and numerical simulation. It was found that downstream effects play an important role, and the results further suggest that the downstream binding profiles may find use in simple affinity evaluation. / QC 20100713

La presente tesis, titulada “Genes, peoples and languages in Central Africa”, examina los patrones de diversidad genética en poblaciones del oeste de Africa central, más específicamente, poblaciones Bantús y Pigmeas de Gabon y Camerún, dos zonas vitales para la comprensión de la expansión Bantú. Se han analizado más de 800 muestras a nivel del cromosoma Y con el fin de caracterizar genéticamente a estas poblaciones, y establecer la relación genética entre ellas. Los resultados han demostrado que la expansión Bantú homogeneizó el acervo genético de las poblaciones Bantús, eliminando la diversidad pre-Bantú, mientras que diversificó aquel de las poblaciones Pigmeas, introduciendo linajes Bantus. Además, se ha visto que el flujo de linajes paternos parece haber tenido una única dirección: de Bantus a Pigmeos. Estos resultados contrastan con aquellos obtenidos para linajes maternos (DNA mitocondrial) en estas zonas, donde se ha observado un considerable flujo genético de Pigmeos a Bantus, sugiriendo un posible sesgo sexual en la tasa de mestizaje entre poblaciones Bantus y Pigmeas. Un hallazgo interesante es la presencia de un linaje no-africano en estas poblaciones de África subsahariana. / The present thesis titled “ Genes, peoples and languages in Central Africa” examines the genetic diversity patterns in populations from west central Africa, more specifically, in Bantu and Pygmy populations from Gabon and Cameroon, two key areas in the understanding of the Bantu expansion. More than 800 samples have been analysed at the Y chromosome level in order to genetically characterise these populations and establish the genetic relationship between them. The results have shown that the Bantu expansion largely homogenised the gene pool of Bantu populations, erasing the pre-Bantu diversity, while it diversified that of Pygmy groups, introducing Bantu lineages into their gene pool. Furthermore, gene flow of paternal lineages seems to have taken place mainly in one direction; from Bantus to Pygmies. These results contrast with those found in studies of maternal (mtDNA) lineages in these areas, where considerable gene flow from Pygmy to Bantu populations have been observed, suggesting possible sex-biased admixtures rates between Bantu and Pygmy populations. An interesting finding, is the significant presence of a non-African lineage in these sub-Saharan populations.

From a fresh data science perspective, this thesis discusses the prediction of coronary artery disease based on Single-Nucleotide Polymorphisms (SNPs) from the Ontario Heart Genomics Study (OHGS). First, the thesis explains the k-Nearest Neighbour (k-NN) and Random Forest learning algorithms, and includes a complete proof that k-NN is universally consistent in finite dimensional normed vector spaces. Second, the thesis introduces two dimensionality reduction techniques: Random Projections and a new method termed Mass Transportation Distance (MTD) Feature Selection. Then, this thesis compares the performance of Random Projections with k-NN against MTD Feature Selection and Random Forest for predicting artery disease. Results demonstrate that MTD Feature Selection with Random Forest is superior to Random Projections and k-NN. Random Forest is able to obtain an accuracy of 0.6660 and an area under the ROC curve of 0.8562 on the OHGS dataset, when 3335 SNPs are selected by MTD Feature Selection for classification. This area is considerably better than the previous high score of 0.608 obtained by Davies et al. in 2010 on the same dataset.

[ES] El melón (Cucumis melo L.) es actualmente uno de los cultivos con mayor importancia económica en el mundo. La amplia variabilidad genética intraespecífica que presenta permite el estudio para su explotación del control genético de un amplio abanico de caracteres tanto agronómicos como de calidad del fruto. En los últimos años se han desarrollado un gran número de marcadores moleculares y de herramientas genómicas en melón, que facilitan el desarrollo de nuevas poblaciones de mejora. Las líneas de introgresión (ILs) son un conjunto de líneas que contienen un fragmento cromosómico de un parental donante, normalmente exótico, en un fondo genético común normalmente de una variedad de élite. Estas colecciones son apropiadas para el estudio de caracteres cuantitativos y para la introducción de alelos exóticos favorables en cultivares comerciales. En la presente tesis doctoral se describe el desarrollo de una colección de ILs empleando la entrada japonesa 'Ginsen makuwa', como parental donante y el cultivar francés 'Vedrantais' como parental recurrente. Los sucesivos genotipados en generaciones tempranas mediante la plataforma Agena Bioscience y High Resolution Melting, han mejorado la eficiencia en el proceso de obtención de las ILs (cinco generaciones). Esta colección incluye 27 ILs, que posteriormente se han caracterizado mediante un genotipado de alta densidad (Genotyping by Sequencing). Éstas presentan un promedio de 2,7 introgresiones/IL con un 94% de recuperación del fondo genético 'Vedrantais', representando un 96,8% del genoma donante. El análisis de los datos de fenotipado en tres ambientes y el genotipado dió lugar a la detección de 86 QTLs (Quantitative Tratit Loci), de los que 74 fueron estables en al menos dos ambientes. De éstos, 3 QTLs están relacionados con aspectos de floración, 4 con la precocidad de maduración del fruto, 33 con aspectos morfológicos (forma del fruto, reticulado y espesor de la corteza), 12 con el proceso de maduración (presencia de aroma, capa de abscisión, firmeza de la pulpa), 16 con el color de la pulpa, 5 con el color interno de la corteza y 1 con el contenido en sólidos solubles. Algunos de los QTLs descritos en esta tesis han sido identificados en trabajos previos, lo que da solidez a las regiones detectadas, otros, en cambio, resultan novedosos y, por tanto, muy interesantes, pues constituyen un recurso muy valioso tanto para la búsqueda de genes candidatos como para el empleo de estos alelos en programas de mejora. De entre las ILs más prometedoras, destaca MAK_10-1 por presentar un bloqueo del climaterio, lo cual se traduce en una mayor vida postcosecha, característica muy buscada en el mercado internacional. Los efectos de la introgresión en el cromosoma 10 son la ausencia de aroma externo y la mayor firmeza de la pulpa, además del mayor contenido de sólidos solubles en pulpa. Además, se han localizado varios genes candidatos involucrados en la regulación transcripcional y de señalización de etileno durante la maduración del fruto. Por otro lado, se describen otras líneas potencialmente interesantes, así como genes candidatos, para proporcionar diversidad de tamaños, formas, color de la pulpa y perfil aromático al mercado de tipos cantalupo. Respecto al perfil de compuestos volátiles (VOCs) analizado en las ILs, se encontró que las introgresiones Makuwa en general disminuyeron el contenido en compuestos aromáticos. A pesar del efecto ambiental notable, se pudieron asociar ciertas regiones genómicas a ciertos perfiles de VOCs, identificando a su vez algunos genes candidatos involucrados en diferentes rutas de biosíntesis de aromas. La dificultad de recuperar ciertos perfiles aromáticos en los programas de mejora se pone de manifiesto por el elevado número de regiones y genes implicados, así como por efectos pleiotrópicos que afectan a la producción de aromas y que se describen en esta tesis como el bloqueo del climaterio o / [EN] Melon (Cucumis melo L.) is one of the most economically important crops in the world. The wide intraspecific genetic variability that it presents allows the study of a wide range agronomic and fruit quality traits. In recent years, a large number of molecular markers and genomic tools have been developed in melon, which is a resource that facilitates the development of new breeding populations. Introgression Lines (ILs) are a set of lines that contain a chromosomal fragment of a donor parent, usually wild or exotic, in a common genetic background usually an elite variety. These collections are appropriate for the study of quantitative traits and, above all, for the introduction of exotic alleles in modern cultivars. This doctoral thesis describes the development of a collection of ILs using the Japanese accesion 'Ginsen makuwa', as an exotic donor parent, and the French cultivar 'Vedrantais' as a recurrent parent. Successive genotyping in early generations through the Agena Bioscience platform and High Resolution Melting, have improved efficiency in the process of obtaining ILs (five generations). This collection includes 27 ILs, which have subsequently been characterized by high-density genotyping (Genotyping by Sequencing). These have an average of 2.7 introgressions / IL with a 94% 'Vedrantais' genetic background, representing 96.8% of the donor genome 'Ginsen makuwa'. The analysis of phenotyping data in three environments and genotyping resulted in the detection of 86 QTLs (Quantitative Tratit Loci), of which 74 were stable in at least two environments. Of these, 3 QTLs related with flowering aspects, 33 QTLs related with the mophological fruit (fruit shape, netting and rind thickness), 12 QTLs related with ripening behaviour (presence/absence of aroma, abscission layer and flesh firmness), 16 QTLs were related with flesh color, 5 QTLs related with color of the inner rind and 1 related with the soluble solid concentration. Some of the QTLs described in this thesis have been identified in previous works, giving greater confidence to the detected regions, others, however, are novel and, therefore, very interesting, becouse they constitute a very valuable resource for the search for candidate genes and for the use of these alleles in improvement programs. Of the entire ILs collection, MAK_10-1 presented a blockade of the climacteric, which can translate into a longer post-harvest life, trait that is very in the international market. The effects of introgression on chromosome 10 are the absence of external aroma and the greater flesh firmness, in addition the higher soluble solids content in flesh. In addition, several candidate genes involved in transcriptional regulation and ethylene signaling during fruit ripening have been located. On the other hand, other potentially interesting lines and candidate genes, are described to provide diversity of sizes, shapes, flesh color and aromatic profile to the cantaloupe type market. Regarding the profile of volatile compounds (VOCs) analyzed in ILs, it was found that Makuwa introgressions generally decreased the content of aromatic compounds. Despite the remarkable environmental effect, certain genomic regions could be associated with certain VOCs profiles, identifying some candidate genes involved in different aromatic biosynthetic pathways. The difficulty of recover certain aromatic profiles in breeding programs is evidenced by the high number of regions and genes involved, as well as by pleiotropic effects that affect the aroma production and which are described in this thesis as the blocking of the climacteric or the flesh color due to the presence of carotenes. / [CA] El meló (Cucumis melo L.) és actualment un dels cultius amb major importància económica en el món. La seua gran variabilitat genètica intraespecífica permet l'estudi per a la seua explotació del control genètic d'un gran ventall de caràcters tant agronòmics com de qualitat del fruit. En els últims anys s'han desenvolupat un gran nombre de marcadors moleculars i de ferramentes genòmiques en meló, que faciliten el desenvolupament de noves poblacions de millora. Les línies de introgressió (ILs) són un conjunt de línies que contenen un fragment cromosòmic d'un parental donant, normalment exòtic, en un fons genètic normalment d'una varietat d'èlit. Estes col·leccions són útils per a l'estudi de caràcters quantitatius, a més de per a la introducció d'al·lels exòtics favorables en cultivars comercials. En la present Tesi Doctoral es descriu el desenvolupament d'una col·lecció d'ILs amb l'entrada japonesa 'Ginsen makuwa' com parental donant i el cultivar francés 'Vedrantais' com parental recurrent. Els successius genotipatges en generacions primerenques, mitjançant la plataforma Agena Bioscience i High Resolution Melting, han millorat l'eficiència en el procés d'obtenció de les ILs (cinc generacions). Esta col·lecció inclueix 27 ILs que posteriorment s'han caracteritzat mitjançant genotipatge per seqüenciació. Estes presenten un promedi de 2,7 introgressions/IL amb un 94% de recuperació del fons genètic 'Vedrantais', representant un 96,8% del genoma donant. L'anàlisi de les dades de fenotipatge en tres ambients i el genotipatge, facilità la detecció de 86 QTLs (Quantitative Trait Loci), dels quals 74 foren estables en al menys dos ambients. D'estos, 3 QTLs estan relacionats amb aspectes de floració, 4 amb la precocitat de maduració del fruit, 33 amb aspectes morfològics (forma del fruit, reticulat, espessor pell), 12 amb el procés de maduració (presència d'aroma, capa d'abscisió, fermesa de la polpa), 16 amb el color de la polpa, 5 amb el color intern de la pell i 1 amb el contingut en sòlids solubles. Alguns dels QTLs descrits en la Tesi han sigut identificats en treballs previs, el que dóna solidesa a les regions detectades, altres en canvi, resulten nous i, per tant, molt interessants, ja que constitueixen un recurs valuós tant per a la recerca de gens candidats com per a l'ús d'estos al·lels en programes de millora. D'entre les ILs prometedores, destaca MAK_10-1 per presentar un bloqueig del climateri, el qual es tradueix en una major vida postcollita, característica molt buscada en el mercat internacional. Els efectes de la introgressió en el cromosoma 10 són l'absència d'aroma extern i la major fermesa de la polpa, a més del major contingut en sòlids solubles. S'han localitzat diversos gens candidats involucrats en la regulació transcripcional i de senyalització d'etilè durant la maduració del fruit. Per altra banda, es descriuen altres línies potencialment interessants, així com gens candidats, per a proporcionar diversitat de grandària, forma, color de la polpa i perfil aromàtic al mercat de tipus cantalupo. Respecte al perfil de compostos volàtils (VOCs) analitzat en les ILs, es trobà que les introgressions Makuwa en general van disminuir el contingut en compostos aromàtics. Malgrat el efecte ambiental notable, es pogueren associar certes regions genòmiques a certs perfils de VOCs, identificant alguns gens candidats en diferents rutes de biosíntesis d'aromes. La dificultat de recuperar certs perfils aromàtics en els programes de millora es posa de manifest per l'elevat nombre de regions i gens implicats, així com pels efectes pleiotròpics que afecten a la producció d'aromes i que es descriuen en esta Tesi, com el bloqueig del climateri o la coloració de la polpa per presència de carotens. / Perpiñá Martín, G. (2020). Desarrollo de líneas de introgresión en melón para la mejora de la calidad de esta especie [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/147113 / TESIS

>Magister Scientiae - MSc / As human beings we are curious about our origin and ancestry. A curiosity has led to an investigation of human evolution and expansion across the world by means of population genetics and phylo-genetics by evaluating a region in Southern Africa that is largely unknown. The objective of this study was to develop a quick, inexpensive and accurate hierarchical diagnostic screening system of the MtDNA phylogenetic tree, AI-SNPs in the mtDNA genome by using High Resolution Melting analysis to evaluate the population composition and ancestral haplogroups of Southern African populations in Limpopo. The admixture between the ‘Khoesan’ hunter-gatherers, herders and the Bantu speaking populations led to population growth and expansion in Limpopo. This has contributed to populations settling in Limpopo and has thus shaped the ancestral contemporary populations. No research on these individuals residing in Limpopo has been done before, thus an investigation of their ancestral origin was necessary. A total of 760 saliva samples were collected from individuals residing in Limpopo. Only 500 saliva samples were extracted by means of an optimized salting out technique. Five hundred extracted genomic samples were genotyped by means of a quick, inexpensive High-resolution melting analysis. Of the 500 samples, the genotyping results showed 95 individuals derived for the L3 haplogroup which gives a 19% ratio of individuals screened with Multiplex 1. Only 56 individuals were derived for the L1 haplogroup, which gives a percentage of 11%. A total of 249 individuals were derived for the L0 haplogroup, making up a 50% of the total individuals genotyped. Only 100 samples were derived for L0a, making up 20% of individuals screened with Multiplex 1. Of the 95 samples derived for the L3 haplogroup, the results showed 87 individuals to be ancestral for both M and N, making up 91.57% of individuals screened with Multiplex 2. http://etd.uwc.ac.za/. In population genetics using SNPs to infer population history and ancestral origin has become significant, this study allowed researchers to evaluate population groups by investigating their genetic markers and the application of the results allowed for downstream analyses. Finally, this study provides a quick and simple screening method for the selection of lineages that are of interest for further studies.

No description available.

Cranberry common bean (Phaseolus vulgaris L.) is planted worldwide and consumed as a critical food source of human protein, fibre, carbohydrates, and minerals. Marsh spot (MS) is a physiogenic disorder which severely impacts seed quality in common beans. Previous studies indicate that MS involves a nutritional disorder caused by Mn deficiency. However, the inheritance and genetic mechanism of MS resistance are still not fully understood. To investigate the genetics of MS resistance, a population of 138 recombinant inbred lines (RILs) was developed from a bi-parental cross between a susceptible cultivar Messina and a resistant cultivar Cran09. The population and its two parents were evaluated for MS resistance during five consecutive years from 2015 to 2019 in both sandy and heavy clay soils in Morden, Manitoba, Canada. The severities of MS were rated and subsequently converted to MS resistance index (MSRI) and MS incidence (MSI). Statistical analyses indicated that MSI and MSRI were highly correlated (r = 0.96-0.99) and had high broad-sense heritability (H²) of 86.5% and 83.2%, respectively. Joint segregation analysis (JSA) of 18 phenotypic datasets from five years and two soil types showed that MS resistance was controlled by four major genes with genetic interactions - one of which may suppress the additive effect of the other three genes. To identify the quantitative trait loci (QTL) and the candidate genes associated with the MS resistance, the 138 RILs and the two parents were sequenced using genotyping by sequencing approach. A total of 52,676 SNPs were detected. After further filtering with a threshold of minor allele frequency > 0.01 and call rate > 20%, 2,061 SNPs were retained and then imputed for genetic map construction and QTL mapping. A genetic map consisting of 2,058 SNP markers on 11 linkage groups or chromosomes was constructed, which covered 1,004 recombination blocks with a total length of 6,449 cM and an average block of 6.42 cM. Three linkage map-based QTL-mapping models ICIM-ADD, ICIM-EPI, and GCIM and one genome-wide association study (GWAS) model RTM-GWAS for 18 phenotypic datasets from different years and soil types were used for identification of QTL. A total of 36 QTL, including 21 of additive and 15 of epistatic effects, were identified. Functional gene annotation analysis revealed 151 Mn-related candidate genes across the common bean reference genome and 17 of them harbored the six QTL discovered in this study. In conclusion, MS resistance in common bean is a highly heritable trait and controlled by several major and minor genes. The results of JSA and QTL mapping advance the current understanding of the genetic mechanisms of MS resistance in cranberry common bean, and provide additional resources for application in genomics-assisted breeding and potential isolation and functional characterization of the candidate genes.

Many countries in the global south - which harbour the majority of the world’s biodiversity - face serious resource limitations and a lack of access to affordable sequencing services. Furthermore, biodiversity research and monitoring of non-model, threatened and/or cryptic species often relies on low-quality non-invasive genetic samples. In situ conservation genomics approaches optimised for field conditions and low-quality DNA can help empower local researchers and meet their needs. To do so, however, accessible and reproducible sequencing and genotyping alternatives are needed. I designed a SNP panel as a field-friendly genotyping approach for two species of Amazonian primates using both high- and low-quality DNA samples, and two different sequencing platforms, Illumina and Nanopore. I used 14 high-quality genomes to identify a set of 210 SNPs that allow for identification of species (twelve SNPs), sex (twelve SNPs) and individual identity (186 SNPs) in two species of tamarins, Leontocebus weddelli and Saguinus imperator. Primers, adapters and indexes were designed in a Genotyping-in-Thousands by sequencing approach that is compatible with both sequencing platforms. This approach is based on sequencing multiplexed PCR products of a few hundred target SNPs to genotype thousands of individuals in a single sequencing run. In an effort to make conservation genomics more accessible, the reproducible pipeline to obtain the informative SNPs is being modulated with Snakemake, a workflow management system. / Muchos países en el sur global - los cuales poseen la mayoría de la biodiversidad mundial - enfrentan serias limitaciones de recursos y una falta de acceso a servicios económicos de secuenciación. Con frecuencia, la investigación y el monitoreo de biodiversidad y especies no-modelo, amenazadas y/o crípticas, dependen de muestras genéticas no-invasivas de baja calidad. La genómica de la conservación in situ optimizada para condiciones de campo y ADN de baja calidad puede empoderar a investigadorxs locales y ayudarles a responder a sus necesidades. Para ello, sin embargo, se requieren alternativas accesibles y reproducibles de secuenciación y genotipado. Diseñé un panel de SNPs como una aproximación de genotipado apta para el campo y dirigida a dos especies de primates amazónicos con el uso de ADN de baja y alta calidad, y dos plataformas de secuenciación (Illumina y Nanopore). Usé 14 genomas de alta calidad para encontrar 210 SNPs que permiten la identificación de la especie (doce SNPs), del sexo (doce SNPs) y de la identidad individual (186 SNPs) en dos especies de pichicos, Leontocebus weddelli y Saguinus imperator. Los cebadores, adaptadores e índices fueron diseñados con un enfoque de Genotyping-in-Thousands by sequencing (Genotipado en los miles por secuenciación) que es compatible con ambas plataformas de secuenciación. Este método está basado en la secuenciación de productos de PCR multiplexados de unos cientos de SNPs para genotipar miles de individuos en una sola corrida de secuenciación. En un intento de mejorar la accesibilidad de la genómica de la conservación, el proceso reproducible para obtener a los SNPs informativos está siendo modulado con Snakemake, un sistema de manejo de flujos de trabajo.

No description available.