Thesis--University of Washington. / Vita. Another copy has number: Thesis 27614. Bibliography: leaves [152]-155.

This thesis is an investigation into the possible genetic background underlying the liability of Standardbred racehorses (Std) to atrial fibrillation (AF). Pedigrees of 204 affected Std admitted to the Ontario Veterinary College Teaching Hospital (OVCTH) for treatment of AF born from 1978 to 2007 and of 1,017 randomly selected racing contemporaries (5 for each Std admitted). Estimates of heritability of AF were obtained using a linear threshold animal model. Marginal genetic contributions of ancestors to affected and control cohorts were determined and differences were tested. The estimate of heritability of AF in the Std was 14% on the observed scale. Eleven ancestors had significantly higher contributions to affected cohorts than to controls. Many of these ancestors appeared multiple times in the five-generation pedigrees of affected horses. Results strongly indicate a genetic predisposition to AF in the Std, with the arrhythmia particularly prevalent in one popular sire line.

The genetic status of the critically endangered Mississippi sandhill crane (Grus canadensis pulla) was analyzed using 2009 studbook data from the U.S. Fish and Wildlife Service managed captive breeding and release program. Microsatellite DNA data provided information on shared founder genotypes, allowing for refined analysis of genetic variation in the population, and informed breeding recommendations. The genetic variation observed in the Mississippi sandhill crane was contrasted with variation observed in the Florida sandhill crane (Grus canadensis pratensis). Results show far less variation in the Mississippi population. Results also suggest that while gene flow no longer occurs between the two populations, the introduction of cranes from the Florida population would help to increase the observed genetic diversity of the Mississippi sandhill crane population.

Submitted by LETÍCIA BORGES JOAQUIM null (leticiajoaquim@gmail.com) on 2016-03-18T19:56:09Z No. of bitstreams: 1 DissertaçãoLeticia.pdf: 1246720 bytes, checksum: 72c61040420200f71667f56d8d424fec (MD5) / Approved for entry into archive by Ana Paula Grisoto (grisotoana@reitoria.unesp.br) on 2016-03-22T12:39:49Z (GMT) No. of bitstreams: 1 joaquim_lb_me_jabo.pdf: 1246720 bytes, checksum: 72c61040420200f71667f56d8d424fec (MD5) / Made available in DSpace on 2016-03-22T12:39:49Z (GMT). No. of bitstreams: 1 joaquim_lb_me_jabo.pdf: 1246720 bytes, checksum: 72c61040420200f71667f56d8d424fec (MD5) Previous issue date: 2016-02-22 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Os painéis de marcadores de alta densidade têm demonstrado a sua funcionalidade nos estudos de estrutura da população e conservação genética. Esses painéis permitem avaliar similaridades no padrão do desequilíbrio de ligação em toda população, assim como informações sobre parentesco da população. Segmentos de homozigose são utilizados como indicativo da estrutura da população e fornecem informações sobre o histórico demográfico e eventos de endogamia da mesma. O objetivo deste trabalho foi estudar a estrutura genômica de uma linhagem sintética base Landrace por meio de (i) análises de desequilíbrio de ligação; (ii) estimação do coeficiente de endogamia utilizando dados genômicos e de pedigree; (iii) análise do número e tamanho de segmentos de homozigose e (iv) determinação da estratificação da população. Foram utilizados registros de 300 fêmeas e 25 machos de uma linhagem fêmea sintética base Landrace genotipados com o painel Illumina PorcineSNP60 v2 BeadChip. A edição dos dados foi realizada no programa PLINK v.1.9 para remoção de marcadores SNPs (“Single Nucleotide Polymorphism”) que falharam em mais de 10% das amostras (“call rate”) e amostras que falharam em mais de 10% dos marcadores. A extensão do desequilíbrio de ligação foi avaliada entre todos os pares SNPs adjacentes presentes nos cromossomos autossômicos por meio da medida r2. O coeficiente de endogamia foi calculado usando registros de pedigree e de dados genômicos. Os segmentos de homozigose foram detectados para os cromossomos autossômicos com o programa computacional PLINK v.1.9, considerando pelo menos 50 SNPs homozigotos dentro de tamanho mínimo de 1.000 Kb por animal, permitindo um SNP heterozigoto e um SNP faltante/perdido dentro de uma janela de 50 SNPs. Os segmentos de homozigose detectados foram utilizados para cálculo do coeficiente de endogamia genômica e como indicativo do histórico da população. A estratificação da população foi avaliada utilizando análises de componentes principais e pelo modelo de ancestralidade por metodologia bayesiana aplicado no programa STRUCTURE. Na análise de ancestralidade foram testados valores de K (número de “clusters”) variando de um a oito usando período de burn-in de 1.000 iterações e Cadeia de Markov e Monte Carlo de 10.000 iterações. As análises foram repetidas dez vezes para cada K e a determinação do melhor número para K foi estimada utilizando a estatística Delta K. O valor médio de r² encontrado para todos os SNPs adjacentes que estão a uma distância menor que 100 Kb foi de 0,291 ± 0,312. Os coeficientes de endogamia médios obtidos a partir dos segmentos de homozigose e de registros de pedigree foram de 0,119 e 0,00011, respectivamente. A baixa correlação (r<0,04) encontrada entre os coeficientes de endogamia pode ser explicada pelo efeito de recombinação gênica sobre aqueles estimados a partir dos segmentos de homozigose que não é considerada nas estimativas obtidas à partir de registros de pedigree e devido aos erros de identificação dos animais no pedigree. A identificação de um grande número de longos segmentos de homozigose pode ser indicativa de endogamia recente na população estudada. O estudo da estratificação da amostra indicou que a mesma estaria dividida em duas populações (k=2), sendo que a separação pode ser explicada pelo cruzamento entre as raças ocidentais e orientais utilizadas na formação da linhagem. Os dados de genotipagem permitiram concluir que a população estudada possui endogamia recente, sugerindo-se que seja priorizado acasalamento entre indivíduos menos aparentados para assegurar a manutenção da diversidade genética. / High-density single nucleotide polymorphism (SNP) panels have been used in genomic studies, such as population structure and conservation genetic studies. These panels allow to assess similarities in the patterns of linkage disequilibrium across populations and to estimate relatedness between populations. Runs of homozygosity are used as indicative of population structure and it provides information about demographic history and recent inbreeding. The aim of this study was to describe the genomic structure of a synthetic Landrace line by (i) linkage disequilibrium (LD) analyses; (ii) inbreeding estimates through pedigree and genomic data; (iii) analysing the number and length of runs of homozygosity (ROH); and (iv) determination of population structure. A total of 300 females and 25 males from synthetic Landrace line were genotyped using Illumina PorcineSNP60 v2 BeadChip. Data editing was performed using PLINK v.1.9. The SNPs and samples with a call rate lower than 0.90 were excluded from the data set. Only the autosomal chromosomes were considered for LD an ROH analyses. The LD between all pairs of SNPs were measured by the means of the genotype correlation coefficient (r²) and it determined the decay of LD with physical distance. The coefficient of inbreeding was calculated using genomic and pedigree data. ROH were detected using PLINK v.1.9 considering the follow parameters: a minimum ROH of 50 SNPs with a minimum length of 1000 (Kb), one heterozygous SNP and one missing SNP were allowed within the sliding window of 50 SNPs. The individual genomic inbreeding and population history were identified from estimated ROH. The population structure was evaluated using principal component analysis and Bayesian admixture model. The number of clusters (K) was tested from two to eight considering a burning period of 1,000 followed by 10,000 Markov chain Monte Carlo repetitions and replicated ten times for each K. The best K was estimated using the Delta K statistic. For all SNPs adjacent less than 100 kilobase (kb) apart, the average r2 was 0.291 ± 0.312. The average inbreeding coefficient, calculated by ROH and pedigree analyses, were 0.119 and 0.00011, respectively. The low correlation between the inbreeding coefficients can be justified by the genetic recombination effect over those estimated from runs of homozygosity that were no considered on the estimates from the traditional pedigree. The high number of long ROH is an evidence of recent inbreeding in this population. The population structure analysis revealed K=2 was the best number of clusters and separation. This result can be explained by the crossbreeding between the Eastern and Western breeds used in the formation of the line. The genotyping data helped confirm that the inbreeding in the studied population is recent, which suggests that mating between individuals less related occurred to ensure the maintenance of genetic diversity.

Landwirtschaftliche Systeme müssen sich immerfort an Druckfaktoren wie Klimawandel und Bevölkerungswachstum anpassen. Hierbei spielt die genetische Vielfalt von Pflanzen eine wichtige Rolle, da diese für die Sicherung der Ernährung und des Einkommens von entscheidender Bedeutung ist. Dennoch wird der wirtschaftliche Wert pflanzengenetischer Ressourcen selten untersucht. Um diese Forschungslücke zu schließen, werden in dieser Arbeit drei Bewertungen vorgestellt, welche die wirtschaftlichen Werte pflanzengenetischer Ressourcen untersuchen. Im Rahmen dieser Dissertation werden zwei verschiedene Agrarsystemen analysiert. Diese unterscheiden sich hinsichtlich des Klimas, der agrarökologischen Bedingungen, der landwirtschaftlichen Praxis, der politischen und ökonomischen Rahmenbedingungen sowie der soziokulturellen Verankerung der Kulturart. Die ersten beiden Analysen befassen sich mit der Züchtung und Produktion von Winterweizen in Deutschland. Charakterisiert sind diese durch ein gemäßigtes Klima und intensive Anbaubedingungen. In diesem System überwiegen moderne Sorten, die in einem formalisierten Züchtungsprozess entstanden sind. Es werden die folgenden Forschungsfragen beantwortet: 1) Was ist der ökonomische Wert, der durch den Austausch von Zuchtmaterial entsteht? und 2) Wie hoch ist der mikroökonomische Wert von Resistenzzüchtung? In der dritten Analyse wird ein weiteres Agrarsystem vorgestellt: Die Andenlandwirtschaft, wo im Hochland unter extensiven Bedingungen eine Vielzahl von Kartoffellandrassen angebaut wird. Dort wird folgende Frage analysiert: 3) Welche Mehrwerte wurden durch die Repatriierung oder Neuverteilung von Kartoffellandrassen erzielt? Diese Analysen zeigen, dass die Verfügbarkeit, der Austausch und die Nutzung von pflanzengenetischen Ressourcen die Agrarproduktion verbessern; es entstehen sowohl sektorale, mikroökonomische als auch ernährungsbezogene und kulturelle Mehrwerte. / Agricultural systems must constantly adapt to pressuring events such as climate change and population growth to maintain and improve production processes in a sustainable manner. Thereby the genetic diversity of plants used in agriculture constitute a strategic asset. Nevertheless, their economic value is often overlooked. To fill this research gap, this thesis presents three assessments that produce more evidence on the economic value of plant genetic resources. Two very distinct agricultural systems are discussed. These differ greatly in terms of climate, agroecological conditions, farming practices, seed systems, political and economic frameworks, and the socio-cultural embeddedness of the crop in question. The first two assessments are concerned with winter wheat (Triticum aestivum) breeding and production in the temperate climate and intensive growing conditions in Germany. Modern cultivars created in a formalized breeding process prevail in this system. The following two research questions are elaborated: 1) What is the economic value of exchanging breeding material? and 2) What is the microeconomic value of resistance breeding? The third assessment presents a different agricultural system: Andean agriculture, where a wide variety of potato landraces (Solanum spp.) are grown extensively in the Peruvian highlands. In this case, the research question I investigated is: 3) What are the benefits of repatriating (i.e., redistributing) potato landraces to Andean farmers? These studies demonstrate that the availability, exchange, and adoption of plant genetic resources, which are well adapted to and culturally embedded in specific agricultural systems, improve the overall quantity and sustainability of agricultural production. These improvements can be translated into sectoral, microeconomic as well as nutritional and cultural benefits.