The ability to identify germplasm and select traits accurately is fundamental to successful plant breeding. Pedigrees and molecular markers facilitate these processes; however misleading experimental results can occur when incorrect relationships and/or cultivar names are recorded. Molecular markers can identify these inconsistencies, and with advances in genotyping technology these diagnostics can be done faster and more objectively. This study aimed to develop molecular marker assays and graphical genotyping methodologies for cultivar identification, seed purity assessment and trait selection in oat (Avena sativa L.). KBioscience’s Allele-Specific PCR (KASP™) and genotyping-by-sequencing (GBS) technologies were applied to a set of current Canadian oat cultivars to evaluate their utility for identifying cultivars and detecting intra-cultivar variation. Both KASP™ and GBS detected different extents of heterogeneity among a set of 160 seeds that originated from four seed sources of four cultivars. In both cases, the detected variation did not appear to be limited to a specific cultivar or seed source, reinforcing that all cultivars are heterogeneous. Graphical genotyping localized heterogeneity to specific chromosome regions, thereby distinguishing physical contamination from true genetic heterogeneity and heterozygosity. Pre-existing genotype data for 700 oat cultivars and breeding lines were also used to construct graphical genotypes for pedigree validation and discovery of potential sources for favourable quantitative trait loci (QTL) alleles. This methodology used historical QTLs and anchoring markers to identify 25 putative “high oil” allele carriers. The results from this study will provide diagnostic tools for cultivar identification and pedigree validation, in addition to meaningful information about existing heterogeneity and possible QTL locations in current cultivars.

Abstract Frontotemporal lobar degeneration (FTLD) is the second most common neurodegenerative disease leading to early-onset dementia (< 65 years), next to Alzheimer’s disease. FTLD is substantially a genetic disorder with up to 50% of cases having a positive family history. Mutations in the genes microtubule-associated protein tau (MAPT) and progranulin (PGRN) account for about 10–20% of all cases of FTLD. Hexanucleotide repeat expansion mutation within the gene C9ORF72 has recently been identified as the major cause of FTLD, FTLD with amyotrophic lateral sclerosis (ALS) and pure ALS. During this study, hexanucleotide repeat expansion within the C9ORF72 gene was shown to explain nearly 50% of familial and 30% of all FTLD cases in the Finnish population. Otherwise, the genetic background of Finnish FTLD is largely unknown. The object of the present work was to disentangle the genetic aetiology of FTLD in the Finnish population. We studied a cohort of patients with a clinical diagnosis of FTLD from the province of Northern Ostrobothnia, Finland. Sequencing analysis of the genes MAPT, charged multi-vesicular body protein 2B (CHMP2B) and TAR DNA binding protein (TARDBP) were performed and the MAPT haplotypes were analysed. Correlations between genotype and phenotype were studied in patients with C9ORF72 repeat expansion mutation. C9ORF72 expansion mutation explained nearly 30% of cases of FTLD in our cohort. Concomitant ALS and positive family history of the disease increased the possibility of carrying expanded C9ORF72. The clinical phenotype of C9ORF72 expansion carriers varied at presentation: both behavioural and language variants were detected with or without ALS. The behavioural presentations included prominent psychotic features, although psychiatric presentations were not overrepresented in expansion carriers. No pathogenic mutations were identified in the MAPT, CHMP2B and TARDBP genes in our series of FTLD patients. The H2 MAPT haplotype was associated with FTLD in the series. Our findings emphasise the importance of C9ORF72 expansion mutation in FTLD. While mutations in MAPT and PGRN cause a significant proportion of cases of FTLD worldwide, they seem to be rare causes of FTLD in the Finnish population. Besides being infrequent in other populations, mutations in CHMP2B and TARDBP are rare causes of FTLD in the Finnish population as well. Our findings have clinical implications for recognising phenotypic features characteristic of expanded C9ORF72 as well as for genetic counselling of Finnish patients with FTLD. Even though a considerable proportion of our cases of familial FTLD is caused by the C9ORF72 expansion, over 50 % of our familial cases are without a molecular genetic diagnosis, suggesting that there are other unidentified causal genes to be found. / Tiivistelmä Otsa-ohimolohkorappeumat on toiseksi yleisin työikäisten dementiaa aiheuttava etenevä aivojen rappeumasairaus. Toisinaan otsa-ohimolohkorappeumat esiintyvät yhdessä liikehermorappeuman, amyotrofisen lateraaliskleroosin (ALS), kanssa. Perinnöllisillä tekijöillä on todennäköisesti keskeinen merkitys taudin taustalla. Mutaatiot microtubule-associated protein tau (MAPT)- ja progranulin (PGRN) geeneissä aiheuttavat yhteensä 10–20 % otsa-ohimolohkorappeumista maailmalla. C9ORF72-geenissä sijaitsevan toistojaksomonistuman on vastikään todettu olevan yleisin otsa-ohimolohkorappeumia ja ALS:a aiheuttava mutaatio. Mutaatio on erityisen yleinen suomalaisessa väestössä selittäen lähes 50 % suvuittaisista ja 30 % kaikista otsa-ohimolohkorappeumista. Oireyhtymän perinnöllisyys on muutoin huonosti tunnettu suomalaisessa väestössä. Tutkimuksen tavoitteena oli selvittää otsa-ohimolohkorappeumien geneettisiä syitä aineistossa, joka koostui vuosina 1999–2010 Oulun yliopistollisessa sairaalassa tutkituista potilaista. Tutkimuksessa selvitettiin MAPT-, charged multi-vesicular body protein 2B (CHMP2B)- ja TAR DNA-binding protein (TARDBP) geenien mutaatioiden esiintyvyyttä ja määritettiin MAPT-geenin haplotyypit. Lisäksi tutkittiin taudin kliinisiä erityispiirteitä C9ORF72-mutaation kantajilla. C9ORF72-mutaatio selitti lähes 30 % otsa-ohimolohkorappeumista aineistossamme. Tutkimuksessa havaittiin, että suvuittain esiintyvä tautimuoto ja ALS yhdistyneenä otsa-ohimolohkorappeumaan liittyivät merkittävästi C9ORF72-mutaatioon. Monistuman kantajien fenotyyppi oli moninainen – ensioireina oli sekä käytösongelmia että kielellisiä vaikeuksia. Vaikka C9ORF72-mutaation kantajilla on kuvattu runsaasti psykoottisia oireita, psykoottiset oireet eivät olleet selvästi yliedustettuna mutaation kantajilla aineistossamme. Tutkimuksessa ei löydetty tautia aiheuttavia mutaatioita MAPT-, CHMP2B- tai TARDBP-geeneistä. Havaitsimme kuitenkin tilastollisesti merkittävän yhteyden MAPT-geenin H2-haplotyypin ja otsa-ohimolohkorappeumien välillä. Tuloksemme antavat uutta tietoa C9ORF72-mutaation kantajien kliinisistä erityispiirteistä. MAPT-geenin mutaatioiden merkitys otsa-ohimolohkorappeumien synnyssä ei näyttäisi olevan suomalaisessa väestössä niin merkittävä kuin muissa väestöissä. CHMP2B- ja TARDBP-mutaatiot ovat harvinainen oireyhtymän syy myös suomalaisessa väestössä. Tuloksiamme voidaan hyödyntää suomalaisten otsa-ohimolohkorappeumapotilaiden perinnöllisessä neuvonnassa. Huomattavista edistysaskelista huolimatta yli puolet suvuittain esiintyvistä tautitapauksistamme on vailla geneettistä diagnoosia, mikä antaa aihetta jatkotutkimuksille.

The ability to identify germplasm and select traits accurately is fundamental to successful plant breeding. Pedigrees and molecular markers facilitate these processes; however misleading experimental results can occur when incorrect relationships and/or cultivar names are recorded. Molecular markers can identify these inconsistencies, and with advances in genotyping technology these diagnostics can be done faster and more objectively. This study aimed to develop molecular marker assays and graphical genotyping methodologies for cultivar identification, seed purity assessment and trait selection in oat (Avena sativa L.). KBioscience’s Allele-Specific PCR (KASP™) and genotyping-by-sequencing (GBS) technologies were applied to a set of current Canadian oat cultivars to evaluate their utility for identifying cultivars and detecting intra-cultivar variation. Both KASP™ and GBS detected different extents of heterogeneity among a set of 160 seeds that originated from four seed sources of four cultivars. In both cases, the detected variation did not appear to be limited to a specific cultivar or seed source, reinforcing that all cultivars are heterogeneous. Graphical genotyping localized heterogeneity to specific chromosome regions, thereby distinguishing physical contamination from true genetic heterogeneity and heterozygosity. Pre-existing genotype data for 700 oat cultivars and breeding lines were also used to construct graphical genotypes for pedigree validation and discovery of potential sources for favourable quantitative trait loci (QTL) alleles. This methodology used historical QTLs and anchoring markers to identify 25 putative “high oil” allele carriers. The results from this study will provide diagnostic tools for cultivar identification and pedigree validation, in addition to meaningful information about existing heterogeneity and possible QTL locations in current cultivars.

No description available.

Die Haplotypspezifische Extraktion (HSE) bietet für die Analyse von männlichen Mischprofilen einen neuen und direkteren Lösungsansatz, in dem die haploiden Y-chromosomalen DNS-Komponenten der einzelnen Individuen bereits vor der Analyse der individual spezifischen Marker separiert werden können und dadurch eine wirkliche physische Trennung erreicht wird. Die HSE verwendet Y-chromosomalen SNPs für die Erstellung allelspezifische Extraktionssonden, die nun gezielt nur die Marker der extrahierten DNS Komponente bzw. einer Person separieren sollen. Dabei werden im Hybridisationsschritt der HSE selektive nur komplett hybridisierte Sonden durch eine Polymerase verlängert. Während der Elongation erfolgt eine Biotinylierung des neu entstehenden Stranges, welcher dann selektiv durch Streptavidin markierte Eisenkügelchen extrahiert werden kann. Erste Durchführungen einer HSE zeigten nur eine sehr schwache bis keine Anreicherung. Während der Optimierung verschiedener Parameter wurde die Schlüsselstellung des Sondendesigns in der HSE-Technik deutlich. Die Ergebnisse zeigten, dass die neu entwickelten Sonden den Trennungserfolg der Mischprobe enorm verbessern und in einigen Fällen sogar zum Ausschluss des konkurrierenden Allels führten. Ein Vergleich der HSE Ergebnisse mit den simulierten Sondenparametern der getesteten Sonden ergab, dass der Extraktionserfolg der Sonde maßgeblich durch das Zusammenspiel von Sondenlänge und GC-Gehalt bestimmt wird. Durch dieses neu gewonnene Verständnis über den Einfluss der einzelnen Sondenparameter auf den Trennungserfolg der Mischprobe, können für künftige HSE Anwendungen Sonden effizienter erstellt und deren Wirksamkeit vorhergesagt werden. Zusätzlich konnte das neu entwickelte Vorhersage-Model der Sondenspezifität auch für weitere Extraktionsorte außerhalb des Y-Chromosoms bestätigt werden. Weiterhin konnte durch die Kombination verschiedener Sonden in einer Multiplex HSE mehrerer Y-chromosomaler Marker gleichzeitig getrennt. / Haplotype-specific extraction (HSE) allows the separation of diploid samples in their haploid components and offers in forensic a new straight forward method to separate Y-chromosomal mixed profiles, consisting of haplotype markers like short tandem repeats (STRs). The advantage of the HSE approach in mixture analysis is the real physical separation of the individual DNA components before the amplification of the STR markers. In order to use the HSE technique for the separation of male DNA mixtures, Y-chromosomal extraction probes were designed to single nucleotide polymorphisms (SNPs), which have been specific for one contributor of the male DNA mixtures. During extraction only complete matched probes are extended by a polymerase which results in the incorporation of biotinylated nucleotides. The synthesized and biotin labeled strand is separated by streptavidin coated magnetic beads. Finally, samples were analyzed by PCR coupled capillary electrophoresis for the detection of the extracted STR markers. First tests of a Y-chromosomal specific extraction showed only little till no enrichment of the targeted alleles. Therefore optimization tests of different parameters were carried out, which revealed the probe design as the key factor of successful HSE. A comparison between simulated probe parameters and their extraction success in HSE showed that the HSE probe efficiency mainly depends of the relation of probe length and GC-contents. Because of the new gained knowledge about the influence of the probe-design on the separation success, probes for future HSE application can be developed faster and cost-effective. The new prediction model for probe-specificity was also successful tested for the extraction of other genome-loci. Furthermore, a multiplex HSE approach was used to separate several STR markers simultaneously in one extraction reaction and therefore achieved the separation of one contributor Y-chromosomal haplotype.

Bisherige Methoden der Haplotyp-Block-Definition zielen entweder auf abwesende Rekombinationsereignisse oder eine effiziente Beschreibung genomischer Variation. Die vorliegende Arbeit definiert Blöcke von Single Nucleotide Polymorphisms (SNP) als Gebiete erhöhten Kopplungsungleichgewichtes (LD). Für dieses Ziel wird ein neues, entropie-basiertes Maß für LD zwischen multiplen Markern/Loci (Normalized Entropy Difference) entwickelt und als eine Multilocus-Erweiterung des paarweisen Maßes r2 charakterisiert. Ein zugehöriger Algorithmus für die Block-Definition wird vorgeschlagen. Seine Evaluierung an einem Datensatz des menschlichen Chromosoms 12 vom Internationalen Haplotype Map Projekt zeigt die Nützlichkeit der abgeleiteten Blöcke in Hinblick auf verschiedene Eigenschaften, einschließlich ihrer chromosomalen Coverage und der Anzahl sowie des Anteils der häufigen Block-Haplotypen. Der wesentliche Einfluß der SNP-Dichte auf die zu entdeckenden LD- und Blockstrukturen wird demonstriert. Der Erfolg von Assoziationsstudien in komplexen Erkrankungen mit Block-Haplotypen als multiallelischen Markern wird davon abhängen, ob die Common Variants/Common Diseases (CV/CD) Hypothese für solche Erkrankungen erfüllt ist. / Current approaches to haplotype block definition target either absent recombination events or the efficient description of genomic variation. This thesis aims to define blocks of single nucleotide polymorphisms (SNP) as areas of elevated linkage disequilibrium (LD). To this end, a new entropy-based measure for LD between multiple markers/loci, the Normalized Entropy Difference, is developed and is characterized as a multilocus extension of the pairwise measure r2. A corresponding algorithm for the block definition is proposed. Its evaluation on a data set of human chromosome 12 from the International Haplotype Map project proves the usefulness of the derived blocks with respect to several features, including their chromosomal coverage and the number and portion of common block haplotypes. The critical role of the SNP density for detectable LD and block structure is demonstrated. The success of association studies in common diseases with block haplotypes serving as multi-allelic markers will depend on whether the Common Variants/Common Diseases (CV/CD) hypothesis holds true for those diseases.

Le système de reconnaissance du partenaire sexuel (SMRS) développé par Paterson est un critère important dans la caractérisation des espèces. Dans ce cadre, l'étude d'un complexe d'espèces de Lépidoptères trouve son intérêt. Au Kenya, le genre Busseola est représenté par trois espèces. B. fusca offre un cas intéressant de passage quasi absolu du compartiment sauvage au compartiment cultivé ; B. phaia et B. segeta s'apparentent à un cas de fidélité à l'hôte endémique. B. phaia et B. segeta partagent leurs aires de répartition avec B. fusca, mais sont isolées par la vallée du Rift et par les plantes-hôtes. B. segeta et B. phaia montre une grande proximité systématique. Nous avons étudier ces taxa au travers d'une approche d'écologie chimique et de phylogénie. La diversité génétique observée chez B. fusca au niveau populationnel n'est pas corrélée avec une variabilité du SMRS. Chez B. phaia et B. segeta, l'étude du SMRS a permis de caractériser les composantes de l'isolement reproducteur. L'analyse phylogénétique combinée à l'écologie chimique a permis d'émettre différentes hypothèses quant au statut d'espèce de B. phaia et B. segeta.

Aquest treball és una contribució als estudis de diversitat del genoma humà i pretén estudiar la variació genètica existent a nivell mundial en dos gens, causants de malaltia, el gen CFTR i el gen GBA, en cromosomes d'individus sans. Mutacions en aquests gens produeixen la fibrosi quística i la malaltia de Gaucher respectivament. La fibrosi quística és la malaltia autosòmica recessiva més comuna en poblacions europees. La malaltia de Gaucher és la malaltia lisosòmica d'acumulació lipídica més freqüent. L'estudi analitza la variació genètica en diferents polimorfismes d'ambdós gens; reconstrueix els haplotips i analitza la seva distribució geogràfica; i analitza l'extensió i distribució geogràfica del desequilibri de lligament entre loci. Pel gen GBA, hem ampliat la regió, abastant fins al gen PKLR (que codifica per a la piruvat quinasa). A més a més, pel cas de CFTR, pot ajudar a entendre l'origen de les mutacions més freqüents causants de fibrosi quística. / This work is a contribution to human genome diversity studies and it aims to study the world-wide genetic variation that exists in two disease genes, CFTR and GBA gene, in healthy chromosomes. Mutations in these genes are known to cause cystic fibrosis and Gaucher disease respectively. Cystic fibrosis is the most common severe autosomal recessive disease in patients of European descent. Gaucher disease is the most frequent lysosomal storage disorder. The study analyzes the genetic variation in CFTR and GBA polymorphisms; estimates haplotype frequencies and describes their geographic distribution; and measures linkage disequilibrium between loci. For GBA gene, we have extended the analysis covering PKLR gene (that encodes for a pyruvate kinase). Moreover, for CFTR gene, we have tried to understand the origin of the most common cystic fibrosis causing mutations.

No description available.

New approaches are needed to manage and analyze the enormous quantity of biological data generated by modern technologies. Existing solutions are often fragmented and uncoordinated and, thus, they require considerable bioinformatics skills from users. Three applications have been developed illustrating different strategies to help users without extensive IT knowledge to take maximum profit from their data. SNPator is an easy-to-use suite that integrates all the usual tools for genetic association studies: from initial quality control procedures to final statistical analysis. CHAVA is an interactive visual application for CNV calling from aCGH data. It presents data in a visual way that helps assessing the quality of the calling and assists in the process of optimization. Haplotype Association Pattern Analysis visually presents data from exhaustive genomic haplotype associations, so that users can recognize patterns of possible associations that cannot be detected by single-SNP tests. / Calen noves aproximacions per la gestió i anàlisi de les enormes quantitats de dades biològiques generades per les tecnologies modernes. Les solucions existents, sovint fragmentaries i descoordinades, requereixen elevats nivells de formació bioinformàtica. Hem desenvolupat tres aplicacions que il•lustren diferents estratègies per ajudar als usuaris no experts en informàtica a aprofitar al màxim les seves dades. SNPator és un paquet de fàcil us que integra les eines usades habitualment en estudis de associació genètica: des del control de qualitat fins les anàlisi estadístiques. CHAVA és una aplicació visual interactiva per a la determinació de CNVs a partir de dades aCGH. Presenta les dades visualment per ajudar a valorar la qualitat de les CNV predites i ajudar a optimitzar-la. Haplotype Pattern Analysis presenta dades d’anàlisi d’associació haplotípica de forma visual per tal que els usuaris puguin reconèixer patrons de associacions que no es possible detectar amb tests de SNPs individuals.