Dissertations / Theses on the topic 'Genetic and Phenotypic Correlations'

O presente trabalho teve como objetivo estimar os parâmetros genéticos e fenotípicos das características de qualidade de carne e de características de desempenho, carcaça e composição corporal em uma linhagem macho de frangos fornecida pela Agroceres Ross Melhoramento Genético de Aves S. A. As aves faziam parte do programa denominado sib test, ou teste de irmãos, aonde são coletadas informações de carcaça dos irmãos dos indivíduos a serem selecionados na referida linhagem, estes chamados de rebanho elite. As características de desempenho analisadas foram peso à seleção (PS), peso ao abate (PA) e medidas de ultra-sonografia de músculo peitoral (US). As características de carcaça analisadas foram o peso de peito (PPEI), o peso eviscerado (PE) e o peso de pernas (PPER) e as características de composição corporal analisadas foram o peso da gordura abdominal (GOR), o peso do fígado (FIG) e o peso do coração (COR). As características de qualidade de carne analisadas foram: medida de pH inicial (pHi), medida de pH em 6 horas após o abate (pH6), medida de pH final (pHf), amplitude inicial de queda de pH (AMi), amplitude final de queda de pH (AMf), teor de luminosidade (L*), teor de vermelho (a*), teor de amarelo (b*), perdas de água por exsudação (EXSU), perdas de água por descongelamento (CONG), perdas de água por cozimento (COZ) e força de cisalhamento (FC). Os componentes de (co) variância foram estimados por verossimilhança restrita, utilizando-se o programa MTDFREML. A matriz de parentesco foi composta por 107.154 animais. Para as características pH6, pHf e L* foram estimados coeficientes de herdabilidade moderados; para as demais características estes coeficientes foram baixos. As estimativas de correlações genéticas obtidas não foram indicativas de associações importantes entre as características de qualidade de carne e as características de desempenho, carcaça e composição corporal, exceto pela seleção a favor de PS, que pode reduzir as perdas de água da carne. As estimativas de correlações genéticas encontradas entre as características de qualidade de carne puderam contribuir para o entendimento dos mecanismos relacionados à qualidade da carne na linhagem analisada, de modo que CONG, FC e L* foram características capazes de trazer respostas correlacionadas favoráveis às demais e em maior ou menor grau apresentarem capacidade de resposta à seleção, recomendando-se sua utilização como critério de seleção quando na existência de necessidade de melhoria na qualidade da carne na linhagem estudada. Contudo, esta necessidade não foi aparente, uma vez que as tendências genéticas das características de qualidade de carne, além de terem sido de pequena magnitude, foram em sua maioria favoráveis à qualidade da carne da linhagem analisada.
This research was conducted to estimate genetic and phenotypic parameters of meat quality, performance, carcass and body composition traits in a male broiler line provided by Agroceres Ross Melhoramento Genético de Aves S. A. Broilers measured belonged to a sib test program, in which data from sibs of the individuals to be selected in this line, called elite flock, are collected. Performance traits analyzed were body weight at selection (PS), body weight at slaughter (PA) and ultrasound records of pectoral muscle (US). Carcass traits analyzed were meat breast weight (PPEI), eviscerated body weight (PE) and leg weight (PPER) and the body composition traits analyzed were abdominal fat weight (GOR), liver weight (FIG) and heart weight (COR). Meat quality traits analyzed were: initial pH measure (pHi), pH measure at 6 hours after slaughter (pH6), final pH measure (pHf), initial range of pH fall (AMi), final range of pH fall (AMf), lightness (L*), redness (a*), yellowness (b*), weep losses (EXSU), drip losses (CONG), shrink losses (COZ) and shear force (FC). (Co) variance components were estimated by restricted maximum likelihood method, using the software MTDFREML. The numerator relationship matrix was composed by 107.154 individuals. For pH6, pHf and L*, moderate heritability coefficients were estimated; for the other traits these coefficients were low. Genetic correlation estimates obtained indicated a small association among meat quality traits and performance, carcass and body composition traits, except for the selection to PS, which seemed to be able to reduce water losses of meat. Genetic correlations estimates among meat quality traits could orientated the understanding of the mechanisms related to meat quality in the analyzed line; CONG, FC and L* seemed to be able to bring favorable correlationed responses, so it was recommended its use as selection criterion if existing the necessity of improving the meat quality in the analyzed line. However, this necessity was not apparent, since the genetic trends of meat quality traits were small and favorable to meat quality in the analyzed broiler line.

Hereditary hearing loss is the most common sensory disorder, affecting 1 in 500 newborns. There are more than 538 million individuals with genetic hearing loss worldwide and this number is expected to grow to 1 billion over the next three decades. Currently, the only option for individuals with hearing loss is mechanical intervention such as hearing aids or cochlear implants. In the past decade, many studies have highlighted the need for personalized gene therapy or molecular intervention to treat genetic deafness. However, in order to fulfill this vision a comprehensive understanding of the intricate mutation-gene-phenotype nuances and relationships is required. Toward this goal, we unraveled novel mutation-gene-phenotype associations and mechanisms in four deafness-causing genes (CIB2, COL11A1, CEACAM16 and DFNA5), by using a combination of in-depth phenotyping, human genetics, cutting edge genomic technologies, murine mutant models, and functional assays. These novel insights revealed mutations in CIB2 do not cause Usher Syndrome, mutations in COL11A1 can cause either non-syndromic or syndromic hearing loss, CEACAM16-related deafness is due to two distinct mechanisms, loss of function and gain of function, and coding variants can influence mRNA assembly and cause DFNA5-related hearing loss. Elucidating these novel mutation-gene-phenotype relationships has improved our knowledge of the pathogenic mechanisms underlying hearing loss and provided much needed answers to individuals seeking a diagnosis for their deafness. Recognizing the complexities associated with genetic hearing loss and the challenges in interpreting the clinical significance of genetic variants, we established the first deafness-specific variant database, the Deafness Variation Database (DVD), which classifies over 876,000 variants across 152 deafness-associated genes. This breadth of data provided us with a unique opportunity to explore the molecular landscape of deafness. We show that over 96% of coding variants are rare and novel and that mutational signatures are unique to each gene and are driven by minor allele frequency thresholds, variant effect, and protein domain. The mutational landscape we define shows complex gene-specific variability, making an understanding of these nuances foundational for improved accuracy in variant interpretation. Overall the work presented in this thesis improves our understanding of deafness biology, identifies novel targets for therapeutics and enhances clinical decision-making.

In long term, to discover the genes responsible for wood production, genetic control of wood specific gravity (WSG) in Pinus brutia Ten. (Turkish red pine) open pollinated Ceyhan progeny trial, which was established with the seeds collected from 168 clones originated from six clonal Turkish red pine seed orchards was studied. Wood samples were taken by destructive sampling during the rouging of this trial at the age of seven. Specifically
(1) to examine the magnitude of family differences and its components for wood specific gravity (WSG) and growth traits (height, diameter and stem volume)
(2) to determine WSG inheritance and its genetic correlation with growth traits
and (3) to estimate breeding values of 168 families for the WSG and to predict genetic gain if selection is based on phenotypic, rouged and genotypic seed orchard by reselecting the best parents with respect to WSG. Differences among the 168 families for mean WSG was large (ranged from 0.35 to 0.44), as indicated by high individual (0.42+0.07) and family mean (0.55+0.03) heritabilities. Family differences and high heritabilities were also observed for all growth traits. Genetic correlations between WSG and growth traits were statistically insignificant (near zero), while low and insignificant negative phenotypic correlations among the same traits were observed. Realized genetic gain for single trait selection at age seven was insignificant (0.37 %) for WSG and 8.4 % for stem volume in phenotypic seed orchards. Average genetic gain in breeding zone after roguing, by leaving the best 20 clones in each seed orchard, reached 1.7 % for WSG and 16.1 % for stem volume. Genetic gain (relative to controls) at the age of seven obtained from the first generation genotypic seed orchards consisting the best 30 clones was estimated 5.2 % for WSG and 35 % for stem volume. Multi-trait selection was also proposed in this study for the same traits. Selection of best 10 families for the highest WSG and stem volume breeding values produce 5.6 % genetic gain for WSG and 27.7 % genetic gain for stem volume. For the future, the 168 families with known phenotypic and genotypic values regarding to WSG will be screened for the genes responsible for wood production.

Risk-taking behavior (RTB) is defined as behavior involving the probability of reward with concurrent probability of some negative outcome. Peer influence is among the most robust predictors of RTB, such that greater peer influence, particularly deviant or delinquent peer influence, is associated with increased RTB. Evidence suggests that those with genetic predispositions for RTB may also be more susceptible to peer influence as a function of genotype. Given that genetic polymorphisms within the dopaminergic system have evidenced associations with various forms of RTB and delinquent peer affiliation, it is possible that these genes may interact with peer influence to predict increased RTB, a process called gene × environment interaction (G×E). We expected that those genetically at risk would take more risks in the presence of a peer than alone. To test this effect, five polymorphisms within the dopaminergic system were genotyped in a sample of 85 undergraduate students. Participants completed a behavioral risk task alone and in the presence of a peer providing "risky" feedback. No significant G×Es were identified for any of the dependent variables. However, participants took significantly more risks in the presence of a risky peer than when taking risks alone. These results suggest that G×E may not be a relevant process for peer-influenced RTB during late adolescence. It is possible that G×E is a relevant process during early adolescence, while gene-environment correlation (rGE) is the dominant process during late adolescence. Future research would benefit from testing whether these genes are relevant to G×E in early adolescence, as well as to rGE during late adolescence.

Objective of the research - to evaluate, using up-to-date statistical–genetic methods, the reproductive characteristics of pig breeds bred in Lithuania, to determine correlation of the characteristics with productivity traits, and to develop an optimised system of pigs genetic evaluation by BLUP method. Tasks of the research was: to determine influence of genetic and non-genetic factors in pigs reproductive characteristics, to evaluate the additive-genetic heritability parameters, and co-response of reproduction traits; to evaluate influence of reproductive characteristics on productivity traits, phenotype and genetic co-response; to develop an optimised pigs genetic evaluation system employing BLUP method, estimating pigs reproductive and productive characteristics, using the integrated multivariate model; to evaluate tendencies of pigs genetic improvement. Novelty of the research: using the method of unifactor and multifactor dispersion analysis, leverage of genetic and non-genetic factors on reproductive characteristics of pigs, breed in Lithuania, was determined; heritability parameters of reproductive characteristics were determined, using modern software; genetic and phenotype co-response of the reproductive characteristics was estimated; genetic correlation between reproductive characteristics and productivity traits was evaluated, using statistical-genetic methods, for the first time in Lithuania; optimised multivariate model for determination of reproductive and... [to full text]

Tese de Doutoramento em Ciências Veterinárias. Especialidade de Produção Animal
Um estudo aprofundado de caracterização genética e estratégias de seleção na raça equina Lusitana foi realizado para identificar os principais fatores que afetam a variabilidade genética desta população e fornecer informações para o delineamento de um programa de melhoramento genético sustentável. Foi analisada a informação genealógica registada entre 1824-2009, incluindo 53417 animais. O intervalo de gerações médio foi de 11.33±5.23 e 9.71±4.48 anos para garanhões e éguas, respetivamente. Os animais nascidos entre 2005 e 2009 tiveram um número médio de gerações conhecidas de 11.20±0.71 e consanguinidade média de 11.34±7.48%. O aumento anual da consanguinidade foi de 0.173±0.070, a que corresponde um tamanho efetivo da população de 28. O número efetivo de fundadores, ascendentes e coudelarias fundadoras foi de 27.5, 11.7 e 5.4, respetivamente. Estes resultados refletem uma forte ênfase em algumas linhas e indicam a necessidade de uma gestão cuidadosa da diversidade genética para o futuro. Foram utilizados modelos mistos para estimar parâmetros genéticos, efeitos fixos e predizer valores genéticos para características morfo-funcionais por análises uni e multivariadas. Os caracteres morfológicos incluídos foram as pontuações parciais atribuídas a mais de 18 mil animais na sua inscrição como reprodutores (classificação de cabeça/pescoço, espádua/garrote, peitoral/costado, dorso/rim, garupa, membros e conjunto de formas), para além da pontuação final (FS), altura ao garrote (HW) e andamentos (GA). Funcionalmente foram considerados os resultados das provas de ensino (WEDT) e maneabilidade (WEMT) em Equitação de Trabalho (WE, cerca de 1500 resultados em 200 cavalos), e Dressage (CD, cerca de 12000 resultados em 760 cavalos). Os efeitos fixos para a morfologia foram a coudelaria, ano, sexo, consanguinidade e idade. Para a funcionalidade foram a prova, nível de competição, sexo, consanguinidade e idade. A heritabilidade estimada (h2) para as pontuações morfológicas parciais variou entre 0.12 e 0.18, à exceção dos membros (0.07). Foi também de 0.18 para FS, 0.61 para HW e 0.17 para GA. Para a performance a h2 foi de 0.32 (WEDT e CD) e 0.18 (WEMT). As correlações genéticas entre os vários componentes parciais de morfologia foram positivas mas muito variáveis (0.08-0.77). As relações genéticas entre morfologia e funcionalidade foram favoráveis, indicando que a morfologia/andamentos podem ser usados como caracteres complementares na seleção para a WE ou CD. A depressão consanguínea foi de magnitude muito reduzida para todos os caracteres analisados. Os valores genéticos estimados para a morfologia e funcionalidade apresentam grande variabilidade, mostrando que a seleção pode ser eficaz, mas a tendência genética observada ao longo dos últimos anos foi moderadamente positiva. Compararam-se ainda duas fontes diferentes de informação (pedigrees vs microssatélites) enquanto indicadores da diversidade genética e estrutura populacional do cavalo Lusitano. Para além das genealogias completas, foram utilizados dados sobre 6 ou 8 microssatélites genotipados em cerca de 19 mil Lusitanos entre 1998-2007. A consanguinidade obtida via genealogias revelou-se melhor estimador da consanguinidade molecular do que o inverso, mas apresentou uma correlação modesta com a heterozigotia multilocus (6% da variabilidade explicada). As taxas de consanguinidade por geração estimadas pelos dois métodos foram semelhantes. As distâncias genéticas entre as principais coudelarias foram comparáveis (correlação entre distâncias genéticas FST de 0.82). Globalmente, os parâmetros calculados a partir de informação genealógica são melhores preditores dos indicadores moleculares. No entanto, ao nível da população, os parâmetros de diversidade genética estimados, tendências ao longo do tempo e subestrutura da população são muito semelhantes quando estimados pelo pedigree ou por marcadores microssatélites.
ABSTRACT - Characterization and selection of the Lusitano horse breed - An in-depth study of characterization and evaluation of selection strategies in the Lusitano horse breed was conducted to identify factors affecting the genetic variability of the breed and provide baseline information for the establishment of a sustainable genetic improvement program. Pedigree records collected in 53417 animals born from 1824 to 2009 were used. The mean generation interval was 11.33±5.23 and 9.71±4.48 years for sires and dams, respectively. For animals born between 2005 and 2009, the mean number of equivalent generations was 11.20±0.71 and the average inbreeding was 11.34±7.48%. The rate of inbreeding per year was 0.173±0.070, and the corresponding effective population size was about 28. The effective number of founders, ancestors and studs was 27.5, 11.7 and 5.4, respectively. These results reflect a strong emphasis placed on a few sire-families and raise concerns regarding the conservation of genetic diversity for the future. Mixed model procedures were used to estimate genetic parameters, fixed effects and genetic trends for morpho-functional traits in Lusitano horses by uni- and multivariate animal models. Morphological traits included were partial scores attributed to more than 18000 horses at the time of registration in the studbook and included the classification of head/neck, shoulder/withers, chest/thorax, back/loin, croup, legs and overall impression, plus a final score (FS) and a score for gaits (GA) and the measurement of height at withers (HW). For functionality, the traits considered were scores obtained in dressage (WEDT) and maneability (WEMT) trials of working equitation (WE, about 1500 records by 200 horses), and classical dressage (CD, about 12130 records by nearly 760 horses). Fixed effects considered in the analyses of morphology, GA and FS were stud, year, sex, inbreeding and age. For functionally traits, the fixed effects were event, level of competition, sex, inbreeding and age. Heritability (h2) estimates for all partial morphological scores ranged between 0.12 and 0.18, except for legs (0.07), and were 0.18 for FS, 0.61 for HW and 0.17 for GA. For performance, h2 was 0.32 for WEDT and CD and 0.18 for WEMT. The genetic correlations among partial components of morphology were positive but widely different (0.08 to 0.77). The favourable genetic relationships existing between morphology and performance indicate that morphology and gaits traits can be used to enhance selection response when the improvement of WE or CD is intended. The magnitude of inbreeding depression was small for all the traits analyzed. The estimated breeding values for morphology, gaits and WE presented a large variability, indicating that selection can be effective, but the genetic trend observed over the last few years was positive but moderate for all traits. The assessment of genetic diversity and population structure obtained by either pedigree data or microsatellite markers was compared. The same pedigree database was used and, in addition, data on either 6 or 8 microsatellite markers genotyped in more than 19000 horses, from 1998-2007. Genealogical inbreeding was a better predictor of molecular inbreeding than the opposite, but it had a modest correlation with multilocus heterozygosity (6% of its variability). Still, the rates of inbreeding per generation estimated by the two methods were very similar. Genetic distances among the major studs producing Lusitano horses were comparable when they were estimated from pedigree or molecular information, with a correlation between FST distances of 0.82, and similar dendrograms were obtained in both cases. Overall, estimates derived from a reduced number of microsatellites or from pedigrees are poorly correlated when considered at the individual level, but parameters derived from pedigree are better predictors of molecular-derived indicators. However, when considered at the breed-level, the estimated diversity parameters, time trends and population substructure are very similar when genealogical data or microsatellite markers are considered.
Instituto Politécnico de Santarém

Amelogenesis imperfecta (AI) is the name given to a clinically and genetically heterogeneous group of enamel biomineralisation defects with Mendelian patterns of inheritance. Enamel quantity and/or quality are affected, with inappropriate retention of enamel matrix proteins in the most cases, resulting in hypoplastic and/or hypomineralised phenotypes. AI most commonly occurs in apparent isolation from other co-segregating clinical abnormalities ('non-syndromic AI'). Instances of AI forming part of a diverse range of syndromes are recognised, but poorly described ('syndromic AI'). To date, reported studies have focused on the X-linked and dominant forms of non-syndromic AI which relate to two enamel matrix proteins (AMELX and ENAM) and more recently a cellular protein of unknown function (FAM83H). Only four mutations in 3 genes (ENAM, KLK4 and MMP20) have been described for autosomal recessive non-syndromic AI. This study aims to gain new insight into the genetic basis and phenotype of autosomal recessively inherited hypomineralised AI, both syndromic and non- syndromic forms, through genetic analysis in consanguineous families. A whole-genome SNP autozygosity screen in a non-syndrmoic AI family of Pakistani origin identified a new locus on chromosome 15q21.3. Sequencing .candidate genes in multiple families revealed four different mutations in the poorly characterised WOR72 gene which resulted in autosomal recessive non-syndromic AI (chapter Ill). Deciduous teeth - VI - extracted as part of clinical care from one individual with homozygous WOR72 mutations, revealed normal enamel rod architecture, yet with abnormal inter-rod enamel revealed by scanning electron microscopy (SEM). Energy-dispersive X- ray (EOX) spectra were characterised by normal carbon (C) and nitrogen (N) peaks, excluding the possibility of retention of enamel matrix protein. However, transverse microradiography (TMR) revealed mineral content values significantly lower when compared to normal teeth, indicating hypomineralisation (chapter Ill). A whole-genome SNP autozygosity screen in a family, with syndromic AI and hypohidrosis identified a second locus on chromosome 11 p15.5- q13.1. Sequencing the exons of every gene within the linked region revealed a missense mutation in the STlM1 gene, which is a calcium ion sensor protein (chapter IV). Analyses of extracted permanent and exfoliated deciduous teeth from the proband patient (VII:3) in family P21 confirmed reduced mineral (as determined by TMR) and increased organic content in enamel (determined by EOX). SEM revealed poor quality enamel prisms which were obscured by an amorphous material. This amorphous material was removed by incubation with a-chymotrypsin, but not by incubation with lipase, which was consistent with the inappropriate presence of protein in the enamel. Western blot analyses of protein extracted from the affected enamel indicated the presence of albumin. The dentine was characterised by abnormal morphology on SEM. The only other clinical abnormality identified was hypohidrosis. In particular, there was no apparent involvement of other ectodermal tissues. 1 } ].

Knowledge of the genetic variation of crop collections is essential for their efficient use in plant breeding programs. The Ethiopian Highland Maize Germplasm Collection Mission was launched throughout the highlands of Ethiopia in 1998 and 287 traditional maize accessions were collected from farmers’ fields. To date, no information was available on the morphological and genetic diversity in this important collection. Various molecular marker techniques and quantitative genetics approaches were applied to accurately unravel the extent of phenotypic and genetic diversity, to study patterns of morphological and molecular variation and to determine association of molecular markers with quantitative trait variation, with the view of designing a sound breeding program and management strategy for maize in the highlands of Ethiopia. The morphological study confirmed that traditional Ethiopian highland maize accessions contain large amounts of variation for agro-morphological traits. The broad trait diversity observed among the accessions suggested ample opportunities for the genetic improvement of the crop through selection directly from the accessions and/ or the development of inbred lines for a future hybrid program. Selection practices followed by local farmers are mostly consistent within agroecology and gave rise to morphologically distinct maize accessions in different agroecologies. This underscores the importance of considering farmers’ knowledge of diversity in the collection and evaluation of local accessions. The results of amplified fragment length polymorphism (AFLP) and microsatellite or simple sequence repeat (SSR) marker analyses showed that bulking leaf samples from 15 individual plants per out-bred accession is an effective means of producing representative profiles of individual plants, thereby reducing the cost of DNA extraction and subsequent marker analysis of open-pollinated varieties. Cluster analyses based on AFLP and SSR data showed that most of the accessions collected from the Northern agroecology were genetically distinct from the Western and Southern accessions suggesting that differentiation for adaptive traits for drought conditions may have occurred in the Northern accessions. However, there was very little genetic differentiation between the Western and Southern accessions suggesting gene flow between the two agroecologies and recent introduction of similar improved varieties in these agroecoogies . In both marker systems, high mean genetic diversity was observed among the traditional Ethiopian highland maize accessions. This is possibly due to (i) the continuous introduction of maize from abroad by different organizations; (ii) genetic variation generated through farmers management practices; and (iii) the presence of different environmental conditions in the highlands of Ethiopia to which local landraces may have been adapted. The correlation between the morphological dissimilarity matrix and the matrices of genetic dissimilarity based on SSR and AFLP markers were 0.43 and 0.39, respectively (p = 0.001 in both cases). The correlation between SSR and AFLP dissimilarity matrices was 0.67 (p = 0.001). These significant correlations indicate that the three independent sets of data likely reflect the same pattern of genetic diversity, and validate the use of the data to calculate the different diversity statistics for Ethiopian highland maize accessions. From this study, three groups of maize accessions with distinctive genetic profiles and morphological traits were identified that will be useful for future collection, conservation and breeding programs of maize for the highlands of Ethiopia. A pilot association study using SSR markers and quantitative trait variation indicated that molecular markers could be useful to identify genetic factors controlling earliness, tallness, grain yield and associated traits, which could be exploited by various breeding schemes. The analytical tools outlined in this dissertation can be a useful tool in managing genetic variation of open-pollinated crops and will aid in the conservation of unique genetic diversity. Production stability and global food security are linked to the conservation and exploitation of worldwide genetic resources and this research attempts to add to that body of knowledge. Copyright 2005, University of Pretoria. All rights reserved. The copyright in this work vests in the University of Pretoria. No part of this work may be reproduced or transmitted in any form or by any means, without the prior written permission of the University of Pretoria. Please cite as follows: Beyene, YA 2005, Genetic analysis of traditional Ethiopian Highland Maize (Zea Mays l.) using molecular markers and morphological traits : implication for breeding and conservation, PhD thesis, University of Pretoria, Pretoria, viewed yymmdd < http://upetd.up.ac.za/thesis/available/etd-02212006-112610 / >
Thesis (PhD (Genetics))--University of Pretoria, 2005.
Genetics
unrestricted

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior
Common bean cultivars development with high nutritional quality joined with grain yield is desirable. In consequence, of this study evaluated the genitors, F1 and its reciprocals, F2 and backcrosses populations obtained in the combination among four genitors. For protein content were used TPS Nobre, Guapo Brilhante, BRS Expedito and UTF-1 Balisa. For fibers content, CNFP 8100, FT 96-1282, Valente and Varre Sai were used. The crossings were performed inside a greenhouse using complete diallel approach and assessed in the field using a randomized complete block design with two replications. The laboratory analyses were realized to protein and dietary fiber content. Negative phenotypic correlation between protein content and grain yield was observed. The crossings between the high protein content genitors produced F2 populations with high protein content. Genetic variability was observed for genitors, F1 s and their reciprocals for dietary fiber content. The largest heritability estimates were obtained for fibers content and the smallest for grain yield. Phenotypic correlation between dietary fiber, their different fractions (soluble and insoluble) and grain yield was not observed. Phenotypic correlation between fiber insoluble and dietary fiber content was positive, wile between soluble and insoluble fiber was negative. In the populations studied, the selection for protein content and fibers associated with high grain yield could be performed with success as long as we have better understanding of the genetic control, environmental effect and genotype x environment interaction that influence these characteristics.
O desenvolvimento de cultivares de feijão com alta qualidade nutricional aliado ao alto rendimento de grãos é desejável. Como conseqüência, este trabalho buscou avaliar os genitores e as populações F1 , recíprocos, F2 e retrocruzamentos obtidos das combinações entre quatro genitores para o teor de proteína (TPS Nobre, Guapo Brilhante, BRS Expedito e UTF-1 Balisa) e de quatro genitores para o teor de fibras (CNFP 8100, FT 96-1282, Valente e Varre Sai). Os cruzamentos foram realizados em casa-de-vegetação, segundo a metodologia de dialelos completos, e avaliados a campo utilizando o delineamento experimental de blocos ao acaso com duas repetições. As análises laboratoriais foram realizadas quanto aos teores de proteína bruta e fibra alimentar. Correlação fenotípica negativa entre proteína bruta e rendimento de grãos foi observada. Hibridações controladas entre genitores com alto teor de proteína, possibilitaram a obtenção de populações F2 com alto teor protéico. Foi encontrada variabilidade genética para teor de fibra alimentar para genitores, F1 s e recíprocos. As maiores estimativas de herdabilidade foram observadas para teor de fibras e as menores para rendimento de grãos. Não foi encontrada correlação fenotípica entre fibra alimentar, suas diferentes frações (solúvel e insolúvel) e rendimento de grãos. As correlações fenotípicas entre o teor de fibra insolúvel e de fibra alimentar foram positivas, enquanto que entre fibra solúvel e insolúvel foram negativas. Nas populações estudadas, a seleção para teor de proteína e de fibras associadas ao elevado rendimento de grãos poderá ser realizada com sucesso, desde que se tenha melhor entendimento do controle genético, dos efeitos ambientais e da interação genótipo x ambiente que atuam nessas características.

Com o intuito de estudar o banco de dados da raça Pardo Suíço Corte no Brasil, foram estimados parâmetros genéticos para características de desenvolvimento ponderal e ganhos de peso pré e pós-desmama, perímetro escrotal e características de carcaça de animais dessa raça e seus cruzamentos, utilizando ultra-sonografia. As características de peso analisadas foram peso ao nascimento (PN), aos 120 dias (P120), aos 205 dias (P205), aos 365 dias (P365), aos 450 dias (P450) e peso aos 550 dias (P550), os ganho de peso analisados foram ganho de peso do nascimento aos 205 dias (GPN205), do nascimento aos 120 dias (GPN120), dos 120 aos 205 dias (GP120205), dos 205 aos 365 dias (GP205365), dos 205 aos 450 dias (GP205450), dos 205 aos 550 dias (GP205550), dos 365 aos 550 dias (GP365550), dos 365 aos 450 dias (GP365450) e ganho de peso dos 450 aos 550 dias (GP450550). Os perímetros escrotais foram analisados aos 205 dias (PE205), aos 365 dias (PE365), e aos 550 dias (PE550). Os componentes de co(variância) foram estimados utilizando-se metodologia de modelo animal completo, com o uso do programa MTDFREML. A matriz de parentesco continha 35.188 animais, sendo 18.688 com registros de produção. Para os pesos pré-desmama os coeficientes de herdabilidade aditiva direta e materna aumentaram sua magnitude do nascimento até a desmama. Nos pesos pós-desmama foi observada grande influência materna até os 550 dias de idade. Pode ser esperada boa resposta à seleção para perímetro escrotal tanto aos 205 como aos 365 dias de idade, havendo alta correlação genética entre estas características. O ganho de peso pré-desmama demonstrou grande influência materna até os 120 dias, e ambiental após esta data. Para o ganho pós-desmama foi observado importante efeito ambiental. A correlação genética entre os pesos foi maior quanto mais próximas foram as pesagens e não foi observada relação importante entre pesos e perímetro escrotal, indicando independência entre estas características. As correlações genéticas entre pesos e ganhos de peso foram maiores entre o ganho e o peso do limite superior do relativo ganho de peso. Devido ao pequeno volume de dados obtidos, estudos complementares são necessários para as características de carcaça. Este estudo possibilitará que seja melhor delineado o programa de melhoramento genético da raça Pardo Suíço Corte no Brasil.
The aim of this study was to investigate a database of the Braunvieh cattle in Brazil, to estimate genetic parameters for growth traits, preweaning and postweaning weight gains and scrotal circumference, as well as carcass traits in purebreed and crossbreed Braunvieh cattle. The growth traits analyzed were birth weight (PN), weight at 120 days (P120), 205 days (P205), 365 days (P365), 450 days (P450) and weight at 550 days (P550), Weight gains traits analyzed were, weight gain between birth and 205 days (GPN205), birth and 120 days (GPN120), 120 and 205 days (GP120205), 205 and 365 days (GP205365), 205 and 450 days (GP205450), 205 and 550 days (GP205550), 365 and 550 days (GP365550), 365 and 450 days (GP365450), 450 and 550 days (GP450550). The scrotal circumference was analyzed at 205 days (PE205), at 365 days (PE365), and at 550 days of age (PE550). The (co)variance components were estimated by full animal model, using MTDFREML program. The relationship matrix contained 35.188 animals, and 18.688 with production records. For the preweaning weights the coefficients of direct and maternal additive heritability increased your magnitude from the birth to weaning. In the postweaning weights were observed great maternal influence until the 550 days of age. Interesting response to selection can be expected to the selection for scrotal circumference realized at 205 and 365 days of age, due to high genetic correlation between these traits. The preweaning gain demonstrated great maternal influence until the 120 days, and environmental effect after this age. For postweaning gain great environmental effect was observed. Genetic correlation between the weights was larger for weights taken in shorter interval. Important relationship was not observed between weights and scrotal circumference, indicating independence between these characteristics. The genetic correlations between weights and weight gains were larger between the gain and the weight of the superior limit of the relative weight gain. Due to small amount of records for carcass traits, further studies are necessary to evaluate them. This study can contribute for the better delineated programs for genetic improvement of Braunvieh cattle in Brazil.

Corneal dystrophies are a group of inherited, primarily monogenic, disorders that compromise the transparency of the cornea and cause visual impairment. A large cohort, consisting of 191 corneal dystrophy probands, was recruited to the study with the aim of investigating the genetic basis of phenotypically heterogeneous corneal dystrophy diagnoses. Following genetic investigation, genotype data was combined with clinical data to investigate genotype-phenotype correlations. The most common cause of corneal dystrophy in this cohort was heterozygous dominant mutations in TGFBI, which were identified in 70 probands with epithelial-stromal dystrophies. The majority of TGFBI mutations displayed genotype-phenotype correlation, however a p.(Gly623Asp) mutation was unexpectedly associated with a broad phenotypic spectrum of disease, including epithelial basement membrane dystrophy (EBMD). There was evidence for additional locus heterogeneity for EBMD; two families were identified in which TGFBI coding mutations were excluded, however no compelling candidate gene(s) were identified following whole exome sequence (WES) analysis. Novel and previously reported mutations in CHST6, UBIAD1 and TACTSD2 were identified for other anterior corneal dystrophies; recessive macular corneal dystrophy, dominant Schnyder corneal dystrophy and recessive gelatinous drop-like dystrophy, respectively. Dominant mutations in ZEB1 were identified in 8 patients with an endothelial dystrophy, posterior polymorphous corneal dystrophy (PPCD3), with novel heterozygous deletions encompassing the ZEB1 gene confirming haploinsufficiency as the mechanism of pathogenicity. Investigation of dominant endothelial dystrophy families using whole genome sequencing (WGS), including PPCD1 and congenital hereditary endothelial dystrophy (CHED1), revealed that mutations in the promoter of OVOL2 are a novel cause of disease and therefore that PPCD1 and CHED1 are allelic disorders. OVOL2 is a transcription factor, which is a direct repressor of ZEB1. OVOL2 was not expressed in normal corneal endothelial cells, therefore it was hypothesised that aberrant expression of OVOL2 in corneal endothelial cells causes transcriptional repression of ZEB1 expression. A novel locus causing dominant PPCD (PPCD4) was identified in a large family from the Czech Republic and linkage analysis and WGS revealed a non-coding mutation in a novel gene as likely to be causative in this family. Interestingly, a proportion of patients clinically diagnosed with a corneal dystrophy were found, on further genetic and clinical investigation, to have an inherited syndrome which was responsible for the presence of corneal opacities, the most common of which was Meretoja syndrome. In some cases, a phenocopy of disease was responsible, including paraproteinemic keratopathy. Genetic screening can therefore significantly improve clinical care for patients and their families. In summary, this study provides insight into the genetic causes of corneal dystrophies including the identification of novel corneal dystrophy genes and mechanisms of disease, which is a pre-requisite for the development of targeted genetic therapies. Furthermore, it provides further understanding of genotype-phenotype correlation for specific corneal dystrophy genes and mutations that can result in improved diagnostic and prognostic accuracy for patients.

Aims: To elucidate the aetiopathological mechanisms underlying the IIMs, through a combination of genotyping, serotyping and clinical phenotyping in a large cohort of Caucasian idiopathic inflammatory myopathy (IIM) patients. Methods: A cross-sectional study of prevalent IIM cases, ascertained through the Adult Onset Myositis Immunogenetic Collaboration, was performed. Cases were confirmed as possessing myositis according to Bohan and Peter (Bohan and Peter 1975a; Bohan and Peter 1975b). IIM clinical subtypes studied included polymyositis (PM), dermatomyositis (DM) and myositis associated with other connective tissue disease (myositis/CTD-overlap). Genotyping of major histocompatibility complex genes, including HLA-B, -DR, -DQ, tumour necrosis factor alpha (TNF-α), was performed using commercial kits. Serotyping of a comprehensive range of myositis specific/associated antibodies (MSA/MAAs) was undertaken. Results: Clinical subsets are described within the serological groupings, suggesting that the classification of the IIMs appears to be better served by the serotype than by the clinical subgrouping of disease. The IIMs possess HLA class I and II haplotype associations and genetic differences observed between PM and DM are accounted for by serological differences. The TNF-308A association is not independent of HLA class I, due to the strong LD within the MHC, but does form part of a haplotype with these factors. An absence of routinely tested for MSA/MAAs makes cancer associated myositis (CAM) more likely, especially in the DM subgroup. An antibody against a 155 and 140kDa doublet is associated with the development of CAM. Outcome measures in the IIMs show construct validity. HLA-DRB1*07 appears to predict a milder clinical phenotype with less disability. No convincing gene-environmental interaction was found capable of altering disease susceptibility or clinical phenotype. Conclusions: Myositis disease subtypes therefore appear to be defined by specific haplotypes acting as risk factors for the development of various MSAs and MAAs.

Mutations in the MMACHC gene cause cblC, the most common inborn error of cobalamin metabolism, with approximately 400 known cases. It results in the inability to convert vitamin B12 (cobalamin) into its two active coenzyme forms, methylcobalamin and adenosylcobalamin, required by methionine synthase and methylmalonyl-CoA mutase respectively. It can be characterized according to age of onset, with early onset patients presenting within the first year of life with a number of pathologies and later onset patients presenting after the age of four with predominantly neurological symptoms. Individuals with the c.394C>T (p.R132X) as well as a number of missense mutations generally have later onset of disease whereas patients with the c.331C>T (p.R111X) and c.271dupA (p.R91KfsX14) mutations usually present in infancy. Expression experiments measuring allele-specific transcripts and quantitative real-time RT-PCR measuring overall MMACHC transcript amount revealed increased transcription from alleles bearing late onset related mutations when compared to early onset mutation-bearing alleles. Understanding the mechanisms underlying early and late onset of disease may improve treatment and prognosis for cblC patients.
cblC, causé par des mutations dans le gène MMACHC, est la maladie génétique la plus commune du métabolisme de la vitamine B12 (cobalamine), avec plus de 400 cas dans le monde. La maladie se traduit par une inhabilité à convertir la cobalamine en deux formes actives de coenzymes nécessaires au bon fonctionnement des cellules chez les mammifères. La première, la méthylcobalamine est nécessaire pour la conversion de l'homocysteine en méthionine par l'enzyme méthionine synthase. La seconde, l'adénosylcobalamine est nécessaire pour la conversion de la méthylmalonyl-CoA en succinyl-CoA par l'enzyme méthylmalonyl-CoA synthase. cblC peut être caractérisé par l'âge d'apparition des symptômes. Les patients qui présentent des symptômes pendant leur première année de vie ont de nombreuses pathologies, alors que les patients qui se présentent les symptômes plus tardivement, après l'âge de quatre ans, ont principalement des affections neurologiques. Les individus avec la mutation c.394C>T (p.R132X) ainsi que ceux avec une mutation faux-sens sont symptomatiques en général plus tard dans leur vie, alors que les individus avec les mutations c.331C>T (p.R111X) et c.271dupA (p.R91KfsX14) le sont habituellement dans leur petite enfance. Dans cette étude, nous avons analysé l'expression spécifique des allèles de MMACHC et mesuré la quantité totale d'ARN messager pour MMACHC. Les résultats montrent que la quantité d'ARN messager est plus élevée pour les allèles reliés à une apparition tardive des symptômes, et que la quantité d'ARN messager total pour MMACHC dans les cellules des patients porteurs des allèles reliés à une apparition tardive des symptômes est-elle aussi plus élevée. Comprendre les mécanismes sous-jacents à l'apparition précoce ou tardive des symptômes de la maladie cblC pourrait nous aider dans le traitement et le pronostic des patients. fr

 

Trypanosoma theileri, of the subgenus Megatrypanum, a non-pathogenic cosmopolitan blood dwelling parasite of bovine. T. theileri can be cultured at room temperature in several culture media.

Blood samples were collected from deer's. To see if the blood was infected with trypanosomes it was cultivated in 2 ml sheep blood or cell cultivation medium DMEM with antibiotics.

Growth was detected by microscopy to see if there were any trypanosomes.

To determine the species of trypanosomes that was in the deer blood a DNA-preparation was done before a Polymerase Chain Reaction (PCR) could be done. With sequencing the trypanosomes where determined to be Trypanosoma theileri.

Different tests were made to see in what way the trypanosomes best were caught to the objective slides.

Forty samples of borrelia positive serum from forty different patients were tested with the fluorescent microscopy. Forty different samples from blood donors were tested the same way.

Blood samples from 16 different fissiped were taken and to see if they were infected with trypanosomes. Three different PCR's were done on the 16 blood samples.

A small test on human blood was also performed.

Protein identification by immunoblot with western blot and silver staining was done.

With the electron microscopy tests were done in the ordinary way and Critical Dry Point to see if both of the techniques worked.

Enzyme-Linked Immuno Sorbent Assay (ELISA) test were accomplished on two 96 well plates. The wells on the plates were diluted in different ways before they were processed.

 

 

Thesis (PhD)--University of Stellenbosch, 2002.
ENGLISH ABSTRACT: This study exploits the Mycobacterium tuberculosis H37Rv genome sequence data in the context of M. tuberculosis clinical isolates, to elucidate genetic variation, and examine the phenotypic and molecular epidemiological implications thereof. The study was initiated by investigation of the insertion sequence IS6110, the primary DNA fingerprinting probe for the molecular epidemiology of tuberculosis. The transposable element is present in variable copy number and chromosomal location in clinical isolates of M. tuberculosis strains, giving rise to extensive genetic diversity. At the inception of this study, little was known about this element in terms of the genetic identity of its surrounding regions, its chromosomal distribution, and the mechanisms contributing to genetic diversity. These shortcomings were therefore addressed by a number of approaches. Firstly, to establish their genetic identity and chromosomal distribution, IS6110 insertion sites from clinical isolates of M. tuberculosis were cloned and sequenced. This data was examined in conjunction with available genome sequence data. The results demonstrated that the majority of insertions occurred within coding regions. Furthermore, the element was shown to have a non-random chromosomal distribution, and a number of preferential integration sites were identified. Secondly, the stability of chromosomal domains flanking IS611 0 elements was investigated by utilizing the insertion site clones as hybridization probes against clinical isolates. This allowed the identification of extensive genetic variation associated with these chromosomal domains, arising from IS6110 transpositions, deletions and point mutations. These events were expressed in terms of a phylogenetic tree which demonstrated ongoing genome evolution associated with IS6110. Thirdly, to investigate the hypothesis that IS6110-mediated deletions occur via homologous recombination between adjacent elements, deletion junctions were mapped and sequenced in clinical isolates representing predecessor and descendant strains. While these results support the involvement of IS6110 as a mediator of genetic deletion, they suggest either alternative mechanisms or the existence of unidentified intermediates. The investigation of IS6110 flanking regions identified the disruption of a number of members of the PPE gene family, leading to the second main area of investigation. The PPE gene family was newly identified as a result of the M. tuberculosis genome sequencing project, and its products are speculated to be of antigenic importance. However, at the commencement of this study very little data was available regarding the biological role of PPE proteins. Therefore, to explore the phenotypic implications of PPE gene disruption, various aspects of the gene family were investigated. Firstly, phylogenetic relationships between members of the PPE family were elucidated, which suggested an evolutionary progression, and highlighted the possibility that there may be functional subdivisions within the gene family. Secondly, the extent and mechanisms of PPE gene variation were analyzed by a combination of hybridization, peR and sequence analysis. This approach revealed extensive variation associated the gene family, although different members of the family exhibit different levels of variation. Of special interest was the discovery that long tandem repeat regions (~69 bp) found within 3 members of the gene family demonstrate variation in the numbers of these tandem repeats. A third avenue of investigation focused on in vitro and in vivo PPE gene expression profiles. RT- , peR was utilized to demonstrate in vitro expression of PPE genes, while RNA:RNA in situ hybridization demonstrated the expression of PPE genes in human tissue samples. Intriguingly, in situ hybridization suggests that there is variable PPE gene expression within the human granuloma. The final approach reported here focused on the subcellular localization of one member of the PPE family, Rv1917c. A combination of cell fractionation and whole-cell antibody binding experiments suggest that the Rv 1917c protein is a cell wallassociated, surface exposed molecule. In summary, the results obtained have potential implications for the interpretation of molecular epidemiological data, support the role of IS6110 as an agent of genome evolution, and emphasize the potential for IS6110 to impact on strain phenotype. Investigation of the PPE family demonstrated that this gene family contributes to genetic variation, is expressed in vitro and in vivo and that at least one protein encoded by the gene family is cell wall associated. Together, the results obtained support the hypothesis that selected members of the PPE gene family may encode products involved in antigenic variation.
AFRIKAANSE OPSOMMING: Dié studie maak gebruik van die Mycobacterium tuberculosis H37Rv genoom volgorde data in die konteks van M. tuberculosis kliniese isolate, om genetiese variasie toe te lig en die fenotipiese en molekulêre epidemiologiese implikasies daarvan te ondersoek. Die studie het 'n aanvang geneem deur die ondersoek van die inset-volgorde /S6110, wat die primêre DNS vingerafdruk pylfragment vir die molekulêre epidemiologie van tuberkulose is. Hierdie transponerende element is in wisselende kopiegetal en chromosomale posisies teenwoordig in kliniese isolate van M. tuberculosis stamme, en gee so oorsprong aan omvangryke genetiese afwisseling. Met die aanvang van hierdie studie was min bekend omtrent hierdie element betreffende die genetiese identiteit van die areas wat die insetsels omring, die chromosomale distribusie van insetsels, asook die meganismes wat bydra tot genetiese afwisseling. Hierdie gebreke is dus deur 'n aantal benaderings aangespreek. Eerstens is IS6110 insettingsetels van kliniese M. tuberculosis isolate gekloneer en hul nukleotiedvolgorde bepaal om sodoende hul genetiese identiteit en chromosomale verspreiding vas te stel. Hierdie data is in oorleg met beskikbare genomiese volgorde data geanaliseer. Die resultate het gewys dat die meerderheid van insetsels binne koderende gebiede plaasgevind het. Verder is gewys dat hierdie element nie na willekeur deur die chromosoom versprei is nie, en 'n aantal gebiede waar insetting by voorkeur plaasvind, is geïdentifiseer. Tweedens is die stabiliteit van die chromosomale gebiede wat IS6110 elemente flankeer ondersoek deur die insettingsetel klone as pylfragmente te gebruik in hibridisasie van kliniese isolate. Dit het die identifisering van omvangryke genetiese afwisseling binne hierdie chromosomale gebiede, wat ontstaan deur IS611 0 transposisies, delesies en puntmutasies, tot gevolg gehad. Hierdie afwisselings is uitgedruk as 'n filogenetiese boom waarin die voortdurende genomiese evolusie wat geassosieer word met IS6110 gewys word. Derdens, om die teorie dat IS6110-gedrewe delesies deur middel van homoloë rekombinasie tussen naasliggende elemente plaasvind te ondersoek, is die grense van delesies gekarteer en die nukleotiedvolgorde daarvan bepaal in kliniese isolate wat voorganger- en afstammelingstamme verteenwoordig. Alhoewel die resultate die betrokkenheid van IS6110 as 'n bemiddelaar van genetiese delesie ondersteun, stel dit ook die bestaan van of alternatiewe meganismes of van onbekende intermediêre vorme voor. Ondersoek van die IS6110-flankerende gebiede het gelei tot die ontdekking van ontwrigting van 'n aantal gene wat behoort tot die PPE geenfamilie, en het so gelei tot die tweede hoof ondersoek tema. Die PPE geenfamilie is ontdek as gevolg van die M. tuberculosis genoomprojek, en dit word gespekuleer dat die produkte van hierdie gene van antigeniese belang mag wees. Daar was egter met die aanvang van hierdie studie baie min data beskikbaar omtrent die biologiese rol van die PPE proteïene. Om die fenotipiese implikasies van ontwrigting van PPE gene te ondersoek is daar dus ondersoek ingestel na verskeie aspekte van hierdie geenfamilie. Eerstens is filogenetiese verwantskappe tussen lede van die PPE familie bepaal, wat gedui het op 'n evolusionêre progressie en wat ook aangedui het dat daar moontlik funksionele onderverdelings binne hierdie geenfamilie mag bestaan. Tweedens is die omvang en meganismes van PPE geenvariasie geanaliseer deur 'n kombinasie van hibridisasie, PKR en nukleotiedvolgorde analise. Hierdie benadering het omvangryke afwisseling binne hierdie geenfamilie getoon, alhoewel verskillende lede van die familie verskillende vlakke van afwisseling demonstreer. Wat veral interessant was, was die ontdekking dat lang tandem herhalingsvolgordes (~69 bp) wat in 3 lede van hierdie geenfamilie voorkom, variasie toon in die getalle van hierdie tandem herhalingsvolgordes. 'n Derde been van ondersoek het gefokus op in vitro en in vivo PPE geen uitdrukkingsprofiele. RT-PKR is gebruik om te toon dat PPE gene in vitro uitgedruk word, terwyl RNA:RNA in situ hibridisasie getoon het dat PPE gene ook in menslike weefsel uitgedruk word. Interessant genoeg dui in situ hibridisasie daarop dat daar wisselende PPE geen uitdrukking binne die menslike granuloom voorkom. Die laaste benadering wat hier gerapporteer word fokus op die sub-sellulêre lokalisering van een lid van die PPE familie, Rv1917c. 'n Kombinasie van selfraksionering en heel-sel antiliggaam-bindingseksperimente dui daarop dat Rv1917c 'n selwand-geassosieerde molekuul is wat aan die oppervlak blootgestel word. Ter opsomming het die resultate wat bereik IS potensiële implikasies vir die interpretasie van molekulêr-epidemiologiese data, dit ondersteun die rol van IS6110 as 'n bemiddelaar van genoom evolusie en beklemtoon die potensiaal vir IS6110 om 'n invloed te hê op die fenotipe van die stam. Ondersoek van die PPE familie het getoon dat hierdie geenfamilie bydra tot genetiese afwisseling, dat dit uitgedruk word beide in vitro en in vivo en dat ten minste een lid van hierdie geenfamilie geassossieer word met die selwand. Tesame ondersteun hierdie resultate die teorie dat geselekteerde lede van die PPE geenfamilie wel produkte enkodeer wat betrokke is by antigeniese variasie.

X-linked recessive brachytelephalangic chondrodysplasia punctata (CDPX1) is a disorder of bone development characterized clinically by chondrodysplasia punctata (CDP), nasomaxillary hypoplasia and brachytelephalangy. There is a wide range of clinical severity in affected males. CDPX1 is caused by inherited deficiency of Arylsulfatase E (ARSE), a Golgi enzyme whose natural substrate is unknown and, is inhibited by warfarin, a drug that reduces vitamin K levels. Nevertheless, almost half of the patients with CDPX1 phenotypes do not have identifiable ARSE mutations. Although this could be due to undetected ARSE mutations or genetic heterogeneity, some could be phenocopies due to fetal deficiency of vitamin K in the first trimester of pregnancy. This has been observed with maternal warfarin use and maternal small bowel disease, pancreatitis and severe hyperemesis gravidarum, leading to the belief that fetal vitamin K deficiency could inhibit a normal ARSE enzyme, thus generating CDPX1 phenocopies. In addition, CDPX1 phenocopies are found in offspring of mothers with maternal autoimmune diseases. Since 2008, with the help of the Collaboration Education and Test Translation program (CETT) for CDPX1, 20 novel variations in ARSE and 24 potential phenocopies have been identified. Clinical data on all patients evaluated was collected and analyzed. In order to determine the effect of the variations on protein function, all ARSE mutant constructs were engineered and transiently expressed in COS1 cells. ARSE activity was measured using the fluorogenic artificial substrate, 4-methylumbelliferyl sulfate. Results showed that (1) frequency of ARSE mutation identification in patients with CDPX1 phenotype is ~ 53%, (2) all missense alleles had negligible ARSE activity suggesting they are pathological and, (3) since the mutations are located throughout the protein and patients with gene deletions show the same phenotype as the ones with missense alleles, genotype-phenotype correlations for ARSE are unlikely.
La chondrodysplasia ponctuée brachytelephalangique liée à l'X récessive (CDPX1) est un trouble du développement des os caractérisée cliniquement par la chondrodysplasia ponctuée (CDP), la hypoplasie nasomaxillaire et la brachytelephalangie. Il y a un large éventail de sévérité clinique chez les sujets masculins touchés. CDPX1 est causée par une carence héréditaire de l'Aryl-sulfatase E (ARSE), une enzyme de l'appareil de Golgi dont le substrat naturel est inconnu et est inhibée par la warfarine, un médicament qui réduit les niveaux de vitamine K. Néanmoins, près de la moitié des patients présentant des phénotypes CDPX1 n'ont pas de mutations d'ARSE identifiables. Bien que cela pourrait être dû à des mutations non détectées ou à une hétérogénéité génétique, certains pourraient être phénocopies dues à une carence fœtale en vitamine K durant le premier trimestre de la grossesse. Cela a été observé avec l'utilisation maternelle de la warfarine et la maladie de l'intestin grêle chez la mère, la pancréatite et vomissements incoercibles sévères, conduisant à croire que la carence en vitamine K fœtale pourrait inhiber une enzyme ARSE normale, générant ainsi des phénocopies CDPX1. Depuis 2008, avec l'aide du programme CETT (Collaboration Education and Test Translation program) pour la CDPX1, 20 nouvelles variations dans ARSE et 24 phénocopies potentielles ont été identifiées. Les données cliniques sur tous les patients évalués ont été recueillies et analysées. Afin de déterminer l'effet des variations sur la fonction des protéines, toutes les constructions de mutant ARSE ont été conçues et exprimées de façon transitoire dans les cellules COS1. L'activité d'ARSE a été mesurée en utilisant le substrat fluorogénique artificiel, 4-methylumbelliferyl sulfate. Les résultats ont montré que (1) la fréquence de l'identification de mutation d'ARSE chez les patients ayant le phénotype CDPX1 est de ~53%, (2) que tous les mutants avaient une activité négligeable d'ARSE suggérant qu'ils sont pathologique, (3) que étant donné que la localisation des mutations et que les patients ayant des délétions du gène exhibe le même phénotype que ceux ayant les allèles missense, les corrélations entre génotype et phénotype sont peu probables.

Chronic copper toxicity was found to result in growth hormesis in both C. hvalina and E. pilosa. Tolerance levels of the bryozoans to copper contamination were found to be high in comparison with those of other marine organisms. Generally, both genotype and copper dosage affected growth and sexual functions, but genotype had no affect on organism response to copper. Nonetheless, large differences in responses were detected between the two E. pilosa populations examined. Variation in tentacle number of C. hyalina colonies was found to be very limited and dietary regime was not observed to have a marked influence upon this trait. In contrast, colonies of E. pilosa were found to produce more tentacles per lophophore in optimal dietary conditions. Significant differences were detected between two E. pilosa populations in astogeny, sexual maturity and tentacle number. Laboratory experiments designed to identify the cue for induction of extended (long) medium proximal spines in E. pilosa colonies were unsuccessful. Differences in spine growth were again identified between the two E. pilosa populations from contrasting sites. Reciprocal transplantation demonstrated that `long' spine formation was triggered in colonies previously possessing only `short' spines and vice versa. Flume observations of particle path trajectories imply that spine formation may result in near-colony flow conditions which are more favourable to feeding in high flow velocities. Demographic analysis using the RAPD technique for both C. hyalina and E. pilosa indicate population structuring corresponding to their contrasting modes of larval dispersal. Populations of C. hyalina appear to exhibit considerable genetic differentiation over distancesa s small as 100 m, whereasE . pilosa is characterisedb y high levels of genetic heterogeneity over much larger spatial scales. E. pilosa population differentiation is observed at a site some 80 Km distance, which may be a consequenceo f hydrographic features. Evidence from analysis of mtDNA (COI) and observations on reproductive isolation and morphological differentiation indicate high levels of cryptic speciation amongst globally distributed populations of C. hyalina. It is suggested that the Chilean C. hyalina population is sufficiently different from all other populations examined to be considered a separate species.

This thesis will examine several pure and complex ataxic conditions with a focus on the genetic and neuropathological characterisation of these disorders. These disorders include Hallervorden Spatz syndrome (HSS), infantile neuroaxonal dystrophy (iNAD) both disorders are part of the neurodegeneration with brain iron accumulation (NBIA) spectrum. Mutations in the pantothenate kinase 2 (PANK2) and phopholipase A2 group 6 (PLA2G6) genes contribute to these disorders, respectively. The latter half of the thesis discusses the movement disorders known as the spinocerebellar ataxias (SCAs) with a focus on SCA11 and SCA15. Mutant mouse models of SCA11 and SCA15 with mutations in the tau tubulin kinase 2 (TTBK2) and inositol 1,4,5-triphosphate type 1 receptor (ITPR1) resepectively, were pathologicaly characterised. Each disorder will be discussed in the introductory chapter and an overall summary conclusion at the end.

Substantial evidence suggests that cortical tissue injury plays a key role in the progression of permanent disability in multiple sclerosis (MS). A greater knowledge of factors that drive pathology in the MS cortex is therefore desperately needed in order to develop novel medicines that can ameliorate disease burden in the progressive stage. In the current thesis, we undertake a robust and quantitative analysis of motor cortical neuropathology in a large cohort of post-mortem MS cases. We find that genetic variation at the HLA-DRB1 locus is associated with the extent of cortical demyelinating and inflammatory disease, especially in younger cases. Relevant to cortical neurodegeneration, we identify fibrinogen deposition as a novel component of MS cortical pathology that associates with neuronal loss, show that carriage of HLA- DRB1*15 has a critical impact on the relationship between microglia/macrophage inflammation and cortical neuronal density, and demonstrate disease-relevant changes to motor cortical neuronal glutamic acid decarboxylase expression. Given the myriad subcortical connections of the motor cortex, we have also undertaken an extensive assessment of corticospinal tract lesional burden throughout the neuraxis and find that motor cortical neurodegeneration appears independent of subcortical tissue injury. Taken together, this thesis highlights the importance of genetic variation at the HLA- DRB1 locus to cortical pathologic outcome, and the fundamental contribution of fibrinogen deposition and cortical parenchymal inflammatory factors to neuronal fate.

Molecular genetics has transformed our understanding of disease and is gradually changing the way medicine is practiced. Genetic mapping provides a powerful approach to discover genes and biological processes underlying human disorders. Recent advances in DNA microarray and sequencing technology have significantly increased the power of genetic mapping studies and have ushered in a new era for biomedicine. In this thesis, linkage analysis (including homozygosity mapping), exome sequencing and candidate gene sequencing have been utilised to genetically dissect autosomal recessive retinal disease. Subsequently, clinical findings from patients found to be similar in terms of molecular pathology have been pooled. DNA and basic phenotypic data from over 500 unrelated individuals were available for the project. Disease-causing variants in three genes that have not been previously associated with human recessive disorders are reported: (a) biallelic mutations in TRPM1 abrogate ON bipolar cell function and cause complete congenital stationary night blindness; (b) biallelic mutations in KCNJ13, a gene encoding an inwardly rectifying potassium channel subunit cause Leber congenital amaurosis; (c) biallelic mutations in PLA2G5, a gene encoding group V phospholipase A2, cause benign fleck retina. The consequences of mutations in these and other disease-related genes (RDH5, GRM6, KCNV2, OAT and SAG) on retinal structure (spectral domain optical coherence tomography, fundus autofluorescence imaging) and visual function (electrophysiology, perimetry testing) have been studied; features that may have mechanistic relevance have been identified. Additionally, DNA sequence variation of a highly polymorphic gene (C2ORF71), recently associated with photoreceptor degeneration, has been studied and quantified in patient and control samples. Basic bioinformatics tools to analyse genomic data have been developed (bash, perl, python and R programming languages). Overall, results presented in this thesis contribute to an understanding of Mendelian retinal disease that is not only observational but also mechanistic.

Trees and forests are under increasing threat from pathogens which cause huge economic and ecological damage. The unprecedented global movement of pathogens into new areas creates novel pathosystems, while the changing climate affects the dynamics of endemic pathosystems. Co-evolution within endemic pathosystems affects the genetic composition of hosts and pathogens. Spatial heterogeneity in pathogen pressure leads to genetic variation in disease-related traits among host populations. In contrast, novel hosts or populations are expected to be highly susceptible to exotic pathogens as there has been no evolution of defence responses. Host response to disease can therefore be an indicator of a novel or endemic pathosystem. The long term resilience of forests to pathogens depends on the adaptive capacity of both the host and pathogen species. Establishing the extent of genetic and phenotypic variation within both the host and pathogen is therefore fundamental in understanding past, current and future pathosystem dynamics. The most significant current threat to Scots pine (Pinus sylvestris) is Dothistroma needle blight (DNB) caused by the foliar pathogen Dothistroma septosporum which is assumed to be exotic to Great Britain. This study aimed to increase understanding of the genetic and phenotypic variation in this pathosystem. Results from this study show that there are high levels of variation in the Dothistroma – Pinus pathosystem. Genetic variation, elucidated using neutral genetic markers, mating type specific markers and in vitro analysis of phenotypic variation in D. septosporum collected from Scottish pinewoods, was found to be high: there was high allelic diversity, particularly within plantation forests outside the native pinewood range, and high phenotypic plasticity in response to different temperature treatments. Both mating type idiomorphs were found in one forest which demonstrates their potential for sexual as well as asexual reproduction. There is also tentative evidence from this study that the pathogen is either introduced to Great Britain or that endemic pathogen populations have been augmented with introduced pathogens. Artificial and natural inoculations of native Scots pine provenances with D. septosporum indicate that there is considerable variation in susceptibility to DNB across the native range in Scotland and that variation in this trait is both highly heritable and evolvable. Furthermore, provenance mean susceptibility to DNB is negatively and significantly associated with water-related variables at site of origin, a finding that is potentially indicative of a co-evolutionary history between host and pathogen. Genetic differences among individuals which are ‘resistant’ or ‘susceptible’ to DNB were identified in Pinus radiata for which there has been extensive research in this pathosystem, by comparing the transcriptome sequences of the two phenotypic groups. Nearly half of the genetic differences identified among phenotypes were found in genes with a putative defence function. In conclusion, native Scots pine provenances contain the necessary heritable genetic diversity to evolve a decrease in their susceptibility to D. septosporum through natural selection in response to elevated prevalence of this pathogen. However, implementation of key native pinewood management strategies, including encouraging regeneration in particular, are necessary in order to facilitate the adaptive evolution of native forests to increased levels of DNB. The effectiveness of this response will depend on the rapidity of adaptation of the pathogen. Measures to limit adaptation where possible, including the use of pathogen monitoring and control in nurseries and the limitation of pathogen movement into native pinewoods, should be continued.

Genetic mutation is the ultimate source of new phenotypic variation in populations. The importance of mutation cannot be understated, and constitutes a significant evolutionary force. Although single mutations may have little to no impact on organismal performance or fitness, when multiplied across the total number of potential sites within the genome, mutation can have a large impact. Accurate measurement of the rates, molecular mechanisms, and distributions of effects of mutations are critical for many applications of evolutionary theory. Despite the importance of both deleterious and beneficial mutations, their genome-wide patterns and phenotypic consequences are poorly understood when considering the mitochondrial genome. Mitochondria are organelles that are essential for eukaryotic life. They contain their own genome and generate bioenergy (ATP) necessary to sustain life via the electron transport chain (ETC). Because of their role in eukaryotic physiology, understanding how mitochondrial genetic and phenotypic variation can impact populations and evolutionary outcomes is essential. Past studies have implicated DNA-damaging oxidative stress as a source of mutations within somatic tissue, but there is a gap in knowledge regarding its role in heritable damage within the germ line. In this thesis, I aimed to test this possibility by characterizing the phenotypic and mutational consequences of high intracellular ROS levels caused by mitochondrial ETC genetic damage. I performed experiments using Caenorhabditis elegans ETC mutant, gas-1, and mutation-accumulation (MA) lines generated from this ancestral genotype. I quantified organismal fitness (fecundity and longevity), reactive oxygen species (ROS) levels, mitochondrial membrane potential (delta psi m), and ATP levels in these lines, and compared the results to those from a set of wildtype control lines. I begin with a general introduction to the hypothesis and the C. elegans system in Chapter I. In Chapter II, I report the findings from this work. In short, I found that while gas-1 MA lines began the experiment with low lifetime fecundity in comparison to the wildtype strain, their fecundity showed no further decline as expected, and even exhibited higher fecundity levels on days 3-5 of reproduction relative to the gas-1 progenitor. The gas-1 progenitor exhibited higher rates of ROS compared to wildtype, whereas the MA lines reverted back to wildtype levels; a similar pattern was observed for delta psi m, while ATP levels were low in the gas-1 progenitor and remained low in the MA lines. I interpret these findings in light of high-throughput sequencing results from these lines showing that, while nuclear and mitochondrial DNA mutation rates were equal to wildtype in these lines, the genomic pattern of mutation was highly nonrandom and indicative of selection for beneficial or compensatory sequence changes. Because ROS levels declined to wildtype in the evolved (MA), this study was unable to address whether ROS is a major contributor to heritable mutation in this system. I hypothesize that, in addition to their putatively compensatory genetic changes, gas-1 lineages experienced physiological compensation allowing them to survive, and that this was associated with a "slow living" phenotype. In Chapter III, I summarize general conclusions and implications of this study and end by providing suggestions for further study.

Pour des espèces domestiques communes parmi lesquelles certaines variétés, populations ou races sont menacées d'extinction, le niveau de la population selon laquelle nous devons prendre des mesures est l'objet de recherches dans de nombreux pays. Plusieurs approches ont été développées et utilisées pour comprendre les différents aspects qui contribuent à la différenciation des races et pour l'étude des produits dérivés. Cette thèse se compose de trois contributions. Les objectifs de la première concerne l'étude de la variabilité génétique et l'analyse de la structure de la population dans six races locales italiennes de poulet au sein d’un projet de conservation. On a analysé vingt marqueurs microsatellites dans 337 animaux appartenant à six différentes races: Ermellinata di Rovigo, Robusta Maculata, Robusta Lionata, Pépoi, Padovana et Polverara, une ligne commerciale de poulet a été utilisé comme référence. On a détectés 120 allèles dans l'ensemble de l'échantillon, avec une valeur moyenne de 5.6 plus ou moins 2.1 allèles par locus. Quant aux races locales, l'hétérozygotie observés variaient de 0.240 à 0.413 et celle attendus variaient de 0.243 à 0.463 pour les races Pépoi et Polverara, respectivement. On a observé des écarts de l'équilibre de Hardy-Weinberg pour cinq races ainsi que pour les croisés commerciaux. Dans l'ensemble, la déficience des hétérozygotes dans la population (FIT) résultait 0.427, la valeur moyenne de FIS était de 0.097, tandis que FST était de 0.437, indiquant une forte carence des hétérozygotes due surtout à la division en races. On a utilisé les distances de Reynolds pour dessiner un arbre Neighbor-Joining unrooted, duquel la topologie a fournie des informations sur l’origine génétique de ces races et a confirmé leur histoire connue. La kinship moléculaire estimée entre race variait de 0.559 à 0.769 en mettant en évidence un haut valeur de coancestry. L'analyse de la structure a été réalisée pour mettre en évidence la présence de substructures de la population. Les clusters obtenues séparaient d’une manière nette les animaux en groupes correspondants aux différentes races, sans aucun mélange. L’exception à cette situation étaient les animaux appartenant à la race Polverara, pour laquelle on a rencontré une structure génétique plus complexe. Les résultats ont confirmé l'utilité des marqueurs moléculaires comme les microsatellites, pour la caractérisation des races locales et de monitorage de la diversité génétique dans les programmes de conservation des animaux domestiques. L'objectif de la deuxième contribution a été de décrire les caractéristiques de la carcasse et les caractères qualitatifs de la viande de trois races locales de poulet qui avait, à la maturité, un poids vif moyens, moyen léger et léger. En particulier, l'exploitation commerciale des races étudiées pourraient permettre de développer et de diversifier l'offre aux consommateurs locaux qui ont besoin de différents produits de volaille. L'expérience a impliqué 60 poulets mâles élevés dans un système de production biologique, avec un accès à un espace extérieur avec l'herbe, dans le but d'étudier les caractéristiques de la carcasse et les caractère qualitatifs de la viande de trois races Italiennes avec lente croissance (Ermellinata, Padovana et Pépoi). Les animaux ont été choisis au hasard à éclore, élevés ainsi dans les mêmes conditions et abattus à 190 jours d'âge. Les animaux ont été sectionnés pour mesurer les caractères qualitatifs de la carcasse, après on a analysé des échantillons de poitrine et de cuisse. La race Ermellinata résultait toujours plus lourde que la race Padovana et Pépoi, en ce qui concerne le poids vif, le poids de la carcasse et de la cuisse; en outre, il y avait des différences en ce qui concerne le pourcentage de protéines (Ermellinata > Pépoi et Padovana), la shear force (Padovana < Ermellinata et Pépoi) et cooking loss (Pépoi > Padovana and Ermellinata). Les valeurs de luminosité (L *), l'indice de rouge (a *) et indice de jaune (b *), qui font partie du système de la CIE, montraient une couleur plus claire de viande et plus sombre de peau pour la Padovana par rapport à d’autres races. La composition des acides gras de la poitrine était similaire entre les espèces étudiées, alors que le contenu des acides gras saturés et monoinsaturés dans la race Ermellinata a été respectivement supérieur et inférieur à celui des autres races. Enfin, l’objectif de la troisième contribution a été l’application d’une approche protéomique à l'étude et à la caractérisation des races locales de poulet. L'expriment a impliqué un total de 29 animaux masculins appartenant à des races locales Pépoi, Padovana et Ermellinata di Rovigo. On a analysé des échantillons du muscle pectoral (Pectoralis superficialis). Les fractions contenant la classe de protéines sarcoplasmiques ont été analysés en utilisant l'électrophorèse bidimensionnelle. L'analyse d'image, soutenue par l'analyse statistique, a permis de différencier les individus en groupes selon les similitudes dans l'expression des protéines. Les individus ont été répartis en clusters et en groupes correspondants à la race d’appartenance. L’analyse SAM a permis l'identification du spot plus importante, dont 10 ont été identifiés par spectrométrie de masse en mettant en preuve, bien que préliminaires, les mécanismes des processus qui régissent le processus de différenciation entre les races. Les résultats ont montré une possible utilisation de la protéomique dans le domaine des études concernant la caractérisation de race, et ainsi que dans le domaine de la traçabilité de race ou de produits dérivés, comme une alternative aux analyses génétiques effectuées à travers des marqueurs moléculaires
In common domestic species for which varieties, strains or breeds are in danger of extinction, the population levels at which action needs to be taken are object of research in many countries. Different approaches have been developed and exploited to understand the different aspects that contribute to breed differentiation and to study the typical products that originate from them. The thesis is made up of three contributes. The objectives of the first one were to determine genetic variation and to analyze population structure in six Italian local chicken breeds involved in a conservation program. Twenty microsatellite markers were investigated in 337 animals belonging to six breeds: Ermellinata di Rovigo, Robusta Maculata, Robusta Lionata, Pepoi, Padovana and Polverara; a commercial layer cross was used as reference. One-hundred-twelve alleles were detected in the overall population, with a mean number of 5.6 plus or minus 2.1 alleles per locus. For the local breeds, the observed and expected heterozigosity ranged from a minimum of 0.240 to a maximum of 0.413 and from 0.243 to 0.463 for the Pépoi and Polverara breeds, respectively. Deviation from Hardy-Weinberg equilibrium has been observed in five breeds and in the commercial cross. The overall population heterozygote deficiency FIT, resulted 0.427, the average FIS 0.097, while FST was 0.437, indicating a high heterozygote deficiency mainly due to breed subdivisions. Reynolds distances were used to draw an unrooted Neighbor-Joining tree, which topology gave information on the genetic origin of these breeds and confirmed their known history. The estimated molecular kinship within breed ranged from 0.559 to 0.769, evidencing high coancestry. Structure analysis was performed to detect the presence of population substructures. Inferred clusters corresponded to the different breeds, without presence of admixture. Exception was the Polverara, for which a more complex genetic structure was found. Obtained results confirmed the usefulness of molecular markers, as microsatellites, to characterize local breeds and to monitor genetic diversity in livestock conservation schemes. The objective of the second contribute was to describe carcass characteristics and qualitative meat traits of three local chicken breeds showing, at maturity, light, medium-light, and medium live weights. By the fact, those breeds could permit to extend and diversify consumer’s offer to fit all the local demands in typical diversified poultry products. The experiment involved 60 male chickens reared in an organic production system where housing was an indoor pen with access to a grass paddock was carried out in order to investigate carcass characteristics and qualitative meat traits of three slow-growing Italian local breeds of chicken (Ermellinata, Padovana, and Pépoi). Chicks were randomly selected at hatch, raised together under the same conditions, slaughtered at 190 days of age, dissected for carcass traits and meat was stored for subsequent analysis of breast and thigh meat quality. Ermellinata chickens were consistently heavier than Padovana and Pépoi chickens for live, carcass, thigh weight and there were differences among breeds for protein percentage (Ermellinata > Pépoi and Padovana), shear force (Padovana < Ermellinata and Pépoi), and cooking loss (Pépoi > Padovana and Ermellinata). The CIE system values of lightness (L*), redness (a*), and yellowness (b*) evidenced a distinctive darker and lighter colour of Padovana for meat and skin, respectively. Fatty acid composition of breast was similar among the studied breeds, while saturated and monounsaturated fatty acids contents of Ermellinata were higher and lower, respectively than the other breeds. Aim of the third study was to apply a proteomic approach for characterization of local chicken breeds. The experiment involved a total of 29 males of Pépoi, Padovana, and Ermellinata local chicken breeds. Samples were taken from breast muscle (Pectoralis superficialis). Sarcoplasmic protein fractions of breast muscle were analysed by bidimensional electrophoresis. Image analysis followed by statistical analysis enabled to differentiate groups of individuals on the similarities of protein expression. Individuals were distinguished into clusters and groups, corresponding to the breed of origin. SAM analysis enabled identification of the most relevant spots; 10 of these were identified by Mass Spectrometry revealing preliminary evidences on the mechanics of the breed differentiation process. Results evidenced a possible utilisation of proteomic approach in the field of breed characterization studies as an alternative to genomic analyses performed using molecular markers, both for breed and product traceability purposes

A series of studies were conducted to evaluate genetic and phenotypic aspects of culling, herd life and survival in Quebec Holstein herds. Data consisted of lactation records obtained from the Programme d'Analyse des Troupeaux Laitiers du Quebec (PATLQ) files, which included 2.2 Million records before the editing procedures. The average productive herd life in Quebec herds was approximately 33 months, corresponding to an average replacement rate of MIND, for both milk recording options. Herds enrolled in the PATLQ official option had cows with longer calving intervals and culled their heifers earlier than herds in the owner sampler option. The probability of being culled for each major reason for disposal was assessed by logistic regression models, and it was shown that culling for low production (voluntary) had a clearly descending trend from 1981 to 1994, while involuntary culling (assumed to include all the reasons other than production) increased in importance mainly because of the ascending trends observed for cuffing due to reproductive problems, mastitis and feet and legs problems. Proportion of cows culled for involuntary reasons increased with parity number, but the opposite occurred for culling due to low production. Herds in the official option culled less for mastitis and sold more cows for dairy purposes than owner sampler herds. After these preliminary studies, a sequence of Weibull models were fitted to analyze different aspects of the data. The genetic study of herd life traits focused on differences between sires regarding true and functional herd life, but also described the effect of different explanatory variables on the failure time variable. Heritability for true and functional herd life was, respectively, 0.09 and 0.08 in the log scale and 0.19 and 0.15 in the original scale. The difference in the median survival time of daughters of bulls with extreme proofs for functional herd life was 1.7 lactations. Quebec dairymen use classification fo

Chronic obstructive pulmonary disease (COPD) is a composite of conditions that include an abnormal inflammatory response and emphysema. Cigarette smoking is the main risk factor for developing COPD and mouse models are widely used in the study of smoking induced emphysema. The C57BL/6 mouse strain develops airspace enlargement after chronic smoke exposure, with no change in lung mechanics. The broad objective of this thesis is to try to identify in mice, candidate genes that cause a difference in susceptibility to the development of the disease and to better understand the inflammatory process that occurs in response to smoke exposure.
A detailed introduction to COPD and proposed mechanisms of its pathophysiology are presented in Chapter I.
Chapter II consists of a manuscript containing data comparing the genetic expression profiles and inflammation in lung tissue of mice (C57BL/6) chronically exposed to cigarette smoke, with age-paired controls. The findings presented in Chapter II are discussed in greater detailed in Chapter III.

This thesis examined genetic and phenotypic aspects of production of farmed Red deer in the UK. Heritabilities for weight traits tended to be moderate to high. Selection on weight at a given age will tend to lead to a correlated increase in weight and all ages and has implications for increased calving difficulty and higher maternal overheads. Animals of Wapiti and Eastern European parentage tended to have higher liveweights than those of British parentage pointing to their possible use as 'terminal' sires. Care is needed when selecting hinds to cross with these stags. Older dams were more likely to have a successful pregnancy and calve earlier. Calving traits tended to have low genetic variation. A central performance test was set up to improve across herd linkages. It is concluded that in future the test should start earlier and a lower limit on the weight of animals going on test should be set. The traits that were included in the economic breeding objective for Red deer included number of calves weaned, hind and offspring food consumption, stag calf and hind carcass weight and hind calf liveweight at 15 months. It was concluded that antlercharacteristics should be excluded from the breeding objective as they have no monetary value in the UK deer industry, but they may be included in selection criteria if they can be shown to improve the accuracy of breeding value prediction. Sources of variation in carcass traits and weight traits were investigated using linear body measurements and photographic techniques. Heights and girths were found to be the best predictors of weight traits. Weight was found to be the best predictor of carcass composition. Recommendations are made for future research. These include the setting up of cross breeding and selection experiments for more accurate parameter estimation and the heterotic effects of using Wapiti and animals of European parentage. Farmers are encouraged to use artificial insemination and the BDFA and MAFF are advisedto set up a performance recording scheme.

In the past few years, interferon-induced transmembrane (IFITM) proteins have been identified as important antiviral factors. The current understanding of IFITMs suggests that they localise within distinct cellular compartments from where they exert their broad antiviral role. For example, IFITM1 localises to the plasma membrane and restricts viruses that do not require endocytosis to infect host cells. In contrast, IFITM2 and IFITM3 are found in the early and late endosomes, respectively, and are potent inhibitors of viruses that depend on endosomal pathways for infection. I begin this dissertation by providing some background on the biology and function of IFITM proteins, including details of in vitro assays that have helped elucidate IFITMs role as antiviral factors. I also describe some early candidate-gene association studies that have attempted to correlate genetic variation within these genes with variation in viral restriction. I also describe how genetic association studies have been used more broadly to understand the biology underlying both infectious and non-communicable diseases. Evidence from in vitro, and in vivo work has demonstrated the IFITMs role as potent antiviral factors, however, no genome-wide association study has reported any significant associations to genetic variant in or around these genes. In Chapter 2, I explore reasons why this may be the case and calculate the coverage of IFITM genes by commercially available genotyping arrays. I show that IFITM2 and IFITM3 are amongst the 7% of all protein coding genes with less than 25% common variant (minor allele frequency > 5%) coverage across all arrays. Poor coverage of genetic variation is therefore one explanation for the lack of IFITM associations in GWAS. The lack of coverage in the genotyping arrays led me to explore other tools to capture variation in the IFITM region. I employ a targeted sequencing method using two different sequencing technologies: short-read sequencing (Illumina MiSeq) and single molecule, real-time sequencing (PacBio RS). Conventional pulldown protocols for targeted sequencing have not been designed for single molecule, real-time sequencing at the time, thus in Chapter 3, I provide some details of the optimisation work required to adapt the targeted method for PacBio sequencing. I then assess the performance of the method for both Illumina and PacBio sequencing. In Chapter 4, I apply the targeted sequencing method described in Chapter 3 to test genetic variants in and around IFITM1, IFITM2 and IFITM3 for association with rapid disease progression in HIV. I also explore the contribution of rare genetic variants (MAF < 1%) to this phenotype by testing for a differential enrichment between cases and controls across each of the three genes. Studies in vitro have also reported that IFITM proteins are potent restrictors of dengue virus infection. In Chapter 5, I use genotype data across a cohort of 2,008 Vietnamese children diagnosed with dengue haemorrhagic fever (DHF) and 2,018 cord blood controls to test if common variants are associated with the disease.

Avian poxviruses are important pathogens of both wild and domestic birds and exhibit a large degree of intragenus diversity at a genomic level. These viruses are known to differ in growth characteristics (in vitro and in vivo), virulence, and cross-protection, with little known about the genomic contributions to these differences. Only six isolates from subclades A and B and one from proposed subclade E have had their genomes completely sequenced. These genomes have been shown to exhibit typical poxvirus genome characteristics with conserved central regions and more variable terminal regions, however all isolates exhibit major differences in defined central regions. This study aimed to analyze and characterize novel isolates from South Africa in terms of growth characteristics and phylogenetic relationships. It also added to the pool of genome sequences available for comparative genomic analyses to further investigate genome architecture. Poxvirus isolates from lesser flamingo (Phoenicopterus minor) and African penguin (Spheniscus demersus) were chosen for analysis from a larger pool of donated isolates by comparison of macroscopic growth characteristics on chorioallantoic membranes, membrane histology and phylogenetic analyses based on nucleotide alignment of partial P4b sequences. Flamingopox virus was shown to group in subclade A3, induce membrane thickening and mesodermal hyperplasia while Penguinpox virus grouped in subclade A2, and did not induce membrane thickening or hyperplasia. The genomes of the above isolates were sequenced and compared to other available avipoxvirus genomes. Dotplot comparisons revealed major differences in central regions that have traditionally been thought to be conserved. Further analysis revealed five regions of difference, of varying lengths, spread across the central regions of the various genomes. Although individual gene identities at the nucleotide level did not vary greatly, gene content and synteny between isolates/species at these identified regions were far more divergent than expected. The reasons for these large genomic rearrangements are yet to be elucidated and will need to be considered in future phylogenetic studies and vaccine vector design. Sequencing and analysis of further avian poxvirus genomes will help characterize this complex genus of poxviruses.

Facial attractiveness plays a crucial role in human mate choice, with individuals from both sexes using facial attractiveness cues to some degree when choosing a partner. Although some of the general facial attractiveness preferences have been studied in cross-cultural populations, most of the research focused specifically on Western populations. Most previous studies also approached facial attractiveness solely from a psychological point of view. One notable exception was a recent study by Roberts et al. (2005) in which the authors linked the Human Leococyte Antigen (HLA) system to cues for health and facial attractiveness in males. This study provides fascinating evidence that genes involved in the immune response also signal attractiveness and health. But is this true cross-culturally and across genders? Roberts et al. (2005) used a British population, who compared to other populations worldwide, have relatively few pathogens that routinely challenge their immune response. The first objective of our study was to test the role of the HLA system in an African female population with a high pathogen load. We found that common HLA alleles, that seemingly provide resistance against common pathogens, play a more important role in health measures than heterozygosity per se. However, our results showed these individuals were not necessarily rated more attractive. So which facial cues do individuals from our study population find attractive in the opposite sex? According to this study individuals from both sexes prefer neotenous features in the opposite sex. Interestingly, we found no preference for facial symmetry and only a slight preference for femininity in females. Our findings support the hypothesis by Boothroyd et al. (2005) that preference for femininity is a by-product of preference for neotenous cues. To test if ethnic preference could not play a confounding role in facial attractiveness ratings of the ethnically mixed South African population, we tested ethnic recognition in two abundant South African ethnic groups. Our results showed that individuals from both sexes could not reliably assign ethnicity to facial images of the two groups. Ethnic preference could therefore not play a role in our study. But mate choice does not only depend on cues displayed by the person being observed. Conditional dependent factors, inherent to the observer, influence how choosy they are of potential partners and therefore how attractive they rate members of the opposite sex. We tested the role of three condition dependent factors, age self-perceived attractiveness and relationship status in both sexes. We observed no significant difference in choosiness between males and females. Male choice therefore plays a more important role in human mate choice than previously expected. Furthermore, our study showed that condition dependent factors affect choosiness differently in males and females. Females are generally more sensitive to condition dependent factors, especially self-perceived attractiveness, while males showed no correlation between any of the condition-dependent factors and choosiness. Since HIV is so prevalent in the South African population, we also tested the role of self esteem in predicting sexual risky behaviour. Our results showed that high self-esteem males were more likely to be sexually active after the age of 18, but that males with low self-esteem were more likely to start sexual activity prematurely. We observed no significant correlation for females. These results indicate that HIV prevention campaigns should focus more on behavioural outcomes other than abstinence, instead of challenging the cultural norms, as indicated by the behavior of high self-esteem individuals. In conclusion, this dissertation is based on the first comprehensive study of genetic and conditional cues associated with facial attractiveness and health in an African population. This African population, with its high pathogen load, high diversity and novel cultural background provided many novel findings, which would hopefully contribute to a more universal view of human mate choice.
Dissertation (MSc (Genetics))--University of Pretoria, 2006.
Genetics
unrestricted

Hereditary haemophilia A (HA), an X-linked bleeding disorder, is caused by mutations in the coagulation factor VIII gene (FVIII abbreviates protein, gene symbol F8). The aim of this study was (1) to characterise F8 mutations in HA cohort from Pakistan, (2) to investigate whether in vitro thrombin generation (TG) differs according to mutation type, and (3) to compare haemophilia joint health score (HJHS) and Gilbert score with severity, age, TG and underlying mutation in HA cohort which had minimal access to haemostatic replacement therapy. Methods: One hundred HA individuals and 100 healthy controls were recruited; clinical details were recorded. Results: Phenotypic measurements were re-evaulated in Cardiff; the essential regions of F8 were screened. Ninty two individuals were diagnosed with HA, 7 with haemophilia B and 1 was normal. The F8 defects were characterised and comprised point mutations, inversions and frameshifts. Thirty novel variants were identified. No significant difference was observed in vitro TG between severes with null mutation and those with a missense change. HJHS was strongly correlated with Gilbert score (r =0.98), both were siginificantly higher in severe compared with nonsevere before the age of 12 years (P≤0.01) but not thereafter. According to developmental age (<12 years, 12-16 years and > 16 years), both scores were significantly lower in the youngest group (P≤0.001). In severes there was no correlation between in vitro TG and joint score, no significant difference was observed for either joint score according to the underlying mutation type. Whereas in nonseveres, negative correlation between in vitro TG and joint score was observed. Conclusions: F8 defects in Pakistan is heterogenous; in severe HA in in vitro TG are not influenced by underlying mutation.

Thesis (PhD (Animal Sciences))--Stellenbosch University, 2011.
ENGLISH ABSTRACT: Local pigs in Southern Africa are an important component of resource-based subsistence farming systems and contribute substantially to the improvement of livelihoods of farmers. The objective of the study was to characterise indigenous pigs through the following specific objectives: to characterise the production systems, to give a physical description and to evaluate the genetic differentiation of the indigenous pigs. Surveys were carried out in Chirumhanzu and Mutoko Districts of Zimbabwe, Afred Nzo, OR Tambo and Vhembe districts of South Africa. Blood samples were collected in all of the above and additional three districts in Malawi (Mchinji, Dedza and Salima). The first study showed that most of the indigenous pigs were kept by women. The farmers kept small herd sizes (<7 pigs) to match the available resources. Income was the main determinant of farmer production objectives and breed preference. Several constraints that would militate against in situ conservation included poor quality and quantity of feeds, diseases, lack of housing, lack of markets and lack of support services. The pigs were generally small and black resembling the Windsnyer-Mukota type of pigs. The pigs apparently had a high foraging ability and high thermo-tolerance that made them suitable for production in low-intensity management free range production systems. These types of pigs were distributed throughout the study area. A microsatellite analysis showed high diversity but very little population differentiation among the pig populations from Southern Africa, with 93 % of variety occurring within subpopulations. Development of markets can be a feasible way of mainstreaming the indigenous pigs into the general economy. This will achieve the twin objectives of conserving and improving the breed while, at the same time, benefitting the farmers that keep these genetic resources. Farmers faced similar production constraints and the pigs were similar across the study areas.
AFRIKAANSE OPSOMMING: Plaaslike varke speel ‘n belangrike rol in hulpbron-gebaseerde bestaansboederye in Suider- Afrika, en maak ‘n aansienlike bydrae tot verbetering van die lewensbestaan van bestaansboere. Die studie het die volgende doelwitte: om die produksie van inheemse varke te karakteriseer, die varke fisies te beskryf, en om die genetiese differensiasie van die inheemse varke te evalueer. Opnames is uitgevoer in die Chirumhanzu en Mutoko distrikte van Zimbabwe, Afred Nzo, OR Tambo en Vhembe distrikte in Suid-Afrika. Bloedmonsters is in al die bogenoemde en nog drie distrikte in Malawi (Mchinji, Dedza en Salima) versamel. Die eerste studie het getoon dat die meeste inheemse varke deur vroue aangehou word. Die boere het klein trop groottes vir aanpasbaarheid by die beskikbare hulpbronne. Inkomste en varkras voorkeur was die hoof bepalende faktore vir hierdie boere se produksie doelwitte. Verskeie beperkings wat bots teen in situ instandhouding sluit in swak kwaliteit- en kwantiteit voere, siektes, gebrek aan behuising, die gebrek aan markte en die gebrek aan ondersteunende dienste. Die varke is oor die algemeen klein en swart en vertoon soos die Windsnyer-Mukoto tipe varke. Hierdie varke het blykbaar ‘n hoë voer-soekende vermoë en hitte-verdraagsaamheid wat hulle geskik maak vir die produksie in lae-intensiteit bestuur en vry-weidende produksie sisteme. Hierdie tipe varke was versprei oor die studie area. ‘n Mikrosatelliet analise het aangedui dat daar hoë genetiese variasie is binne die vark populasie, maar daar is klein differensiasie tussen die verskillende vark populasies van Suider-Afrika, met 93% variasie wat voorkom binne sub-populasies. Die ontwikkeling van markte kan ‘n haalbare manier wees om die inheemse varke toegang te gee tot die algemene ekonomie. Hiermee kan beide doelwitte, bewaring en verbetering van hierdie varkras, tergelyktydig bereik word, ten goede van die boere wat hierdie genetiese hulpbronne aanhou.

Estimates of genetic and phenotypic parameters of lifetime performance traits and estimates of correlations between these and first lactation traits were obtained using multitrait mixed model and Restricted Maximum Likelihood (REML) methodologies, and accounting for all known additive genetic relationships amongst animals in sires pedigree. Part-lifetime performance traits, i.e. two-, three, and four-parity totals of yield and profit, were also included in the analysis. Data were on 82,835 Holstein cows, daughters of 703 sires, calving first between September 1979 and December 1984 in the herds enrolled in Quebec Dairy Herd Analysis Service (QDHAS). Lifetime performance records, however, continued through December 1989.
Results of analysis indicated low estimates of heritability for lifetime performance traits, e.g., lifetime production and profit (.11$ sim$.13) and longevity (.07$ sim$.09). However, production per day of productive life traits had moderate heritability (.28$ sim$.32). Estimates of genetic and phenotypic parameters decreased from part-lifetime to total lifetime performance because residual variances increased at a greater rate compared to rate of increase in sire variances. Both genetic and phenotypic correlations amongst lifetime production, lifetime profit and longevity traits were very high and approached unity in all cases.
Estimates of genetic and phenotypic correlations of first lactation production and profit traits with all measures of part and total lifetime performance were positive and high. These correlations decrease from part-lifetime to total lifetime performance due to part to whole relationships.
Estimates of parameters of lifetime performance traits were mostly free of the effects of selection on milk production. Positive and high genetic correlation of first lactation milk yield with all lifetime performance traits indicated that selection on first lactation milk yield alone will improve all measures of lifetime performance. However, some consideration should be given to measures of reproduction and health which may help in improving the longevity of dairy cattle. (Abstract shortened by UMI.)

Introducción El calentamiento global afecta de modo distinto a diferentes especies. Una de las especies en las que se ha documentado una respuesta genética a la adaptación térmica es Drosophila subobscura. Las clinas latitudinales en la frecuencia de muchas inversiones cromosómicas descritas en esta especie en las poblaciones originales del Paleártico y el descubrimiento de patrones clinales paralelos pocos años después de la colonización de América del Sur y del Norte han proporcionado una de las pruebas más convincentes de que las clinas de inversiones son el producto de la selección natural. Sin embargo, se desconoce el tipo de selección responsable del mantenimiento del polimorfismo cromosómico de inversiones asociado a las clinas. Tradicionalmente se han propuesto tres hipótesis selectivas para dar cuenta del polimorfismo cromosómico, las cuales abarcan distintas unidades de selección: el cromosoma, los genes coadaptados ("supergenes") y los genes individuales. Objetivos Para llegar a entender los mecanismos de selección en la especie D. subobscura, en este trabajo se ha estudiado: 1. La distribución de las ordenaciones cromosómicas a lo largo de un gradiente térmico; 2. La variación nucleotídica en seis genes incluidos en las tres ordenaciones cromosómica más frecuentes; 3. La base genética de la preferencia térmica y de la tolerancia al calor en líneas isocromosómicas. Resultados y Conclusiones Las frecuencias de las ordenaciones cromosómicas en general están correlacionadas con el gradiente de temperatura, formando clinas latitudinales. La ordenación OST se correlaciona positivamente con la latitud y su frecuencia aumenta conforme se avanza desde el sur hacia el norte. Inversamente, la frecuencia de O3+4+7 muestra una correlación negativa con la latitud: alcanza su máxima frecuencia en el sur de Europa y desaparece en el norte. La ordenación O3+4 también exhibe una correlación negativa con la latitud. Estas correlaciones indican que la ordenación OST está adaptada al frío, mientras que las otras ordenaciones pueden considerarse adaptadas a temperaturas más elevadas. La variación nucleotídica de las ordenaciones más frecuentes se analizó en dos poblaciones españolas distantes latitudinalmente. Aunque las frecuencias de las inversiones difieren entre ambas poblaciones, no se han detectado sin embargo diferencias nucleotídicas dentro de cada inversión entre las poblaciones. Se ha detectado flujo genético entre las diferentes inversiones, pero éste no es suficiente para evitar la existencia de diferenciación genética significativa entre las inversiones para todos los genes analizados. La diferenciación genética entre las ordenaciones también se detectó mediante el análisis de desequilibrio de ligamiento. Aparte de la baja tasa de recombinación entre las inversiones, la epistasis en eficacia entre algunos genes podría también contribuir a la diferenciación observada. Mediante la aplicación de diversas pruebas de neutralidad, se ha podido detectar la huella de la selección prácticamente en todos los genes analizados, ya sea en regiones codificadoras o no codificadoras. La hipótesis de la adaptación local es la que se ajusta mejor a nuestros datos, o sea, las inversiones mantienen complejos de genes coadaptados en inversiones de D. subobscura. Nuestros resultados corroboran que las ordenaciones del cromosoma O afectan la preferencia térmica en adultos en un gradiente termal producido en el laboratorio, y que moscas que llevan la ordenación OST adaptada al frío muestran una preferencia térmica hacia temperaturas más bajas que aquellas que tienen las ordenaciones O3+4 y O3+4+8 adaptadas al calor. Sin embargo, estas ordenaciones cromosómicas no tienen ningún efecto sobre la tolerancia al calor en adultos y, por lo tanto, podemos suponer que no hay covarianza genética entre ambos rasgos. La preferencia térmica y la tolerancia al calor en las líneas isocromosómicas de D. subobscura parecen pues ser genéticamente independientes, lo que podría impedir una respuesta coherente del comportamiento y la fisiología (es decir, la coadaptación) a la selección térmica.
Background Global warming is affecting many wild species in different ways. One of the species demonstrating thermal adaptation on the population genetic level is Drosophila subobscura. Latitudinal clines in the frequency of many chromosomal inversions of this species were well documented in the original Palearctic populations, and the discovery of parallel clinal patterns a few years after the colonization of South and North Americas provided compelling evidence that the clines evolved by natural selection. However, the selective process maintaining inversions in populations is not yet clear. Traditionally three selective hypotheses have been advanced to explain the maintenance of the chromosomal polymorphism, according to the level of operation of natural selection: chromosome, coadapted genes (“supergenes”) and individual genes. Objectives To distinguish between different hypotheses the following aspects were studied in D. subobscura: 1. The distribution of chromosomal arrangements along the thermal gradient; 2. The nucleotide variation in six genes inside the three most frequent chromosomal inversions; 3. The genetic basis of thermal preference and heat shock tolerance in isochromosomal lines. Results and conclusions The frequencies of the most abundant chromosomal arrangements in general correlated with temperature gradient, forming latitudinal clines. The arrangement OST positively correlated with latitude and its frequency increased from the south to the north. At the same time the frequency of O3+4+7 shows a negative correlation with latitude and reaches its maximum frequency in the south of Europe disappearing in the north. The O3+4 arrangement has a negative correlation with the latitude. Therefore, the arrangement OST is supposed to be cold-adapted while the other arrangements are considered to be warm-adapted. The nucleotide variation of the most frequent chromosome arrangements was analyzed in two distant Spanish populations situated along a latitudinal gradient. No within-inversion genetic differences were detected among populations, which suggest that the gene content along the gradient is rather constant for the various chromosomal arrangements and genetic flow is high. Although gene flux between different inversions was detected, significant genetic differentiation among inversions for all genes was found. Genetic differentiation between arrangements was also detected by linkage disequilibrium analysis, showing significant associations between informative sites when comparing arrangement pairs, which could be explained by low recombination rate between inversions and probable epistasis between some genes. The footprints of selection nearly in all genes, either in coding or noncoding parts, were detected using several neutrality tests. The Local Adaptation hypothesis is the one that fits better to our data and would explain the maintenance of the coadapted gene complexes within inversions in D. subobscura. Our results corroborate that arrangements on chromosome O affect adult thermal preference in a laboratory temperature gradient, with cold-climate OST carriers displaying a lower thermal preference than their warm-climate O3+4 and O3+4+8 counterparts. However, these chromosome arrangements did not have any effect on adult heat tolerance and, hence, we putatively discard a genetic covariance between both traits arising from linkage disequilibrium between genes affecting thermal preference and genes of heat shock resistance. Therefore, thermal preference and heat tolerance in the isochromosomal lines of D. subobscura appear to be genetically independent, which might potentially prevent a coherent response of behavior and physiology (i.e., coadaptation) to thermal selection. If this pattern were general to all chromosomes, then any correlation between thermal preference and heat resistance across latitudinal gradients would likely reflect a pattern of correlated selection rather than genetic correlation.