Le bar (Dicentrarchus labrax) est une espèce majeure de l'aquaculture méditerranéenne, dont la production est passée de presque rien en 1985 à plus de 100 000 tonnes annuelles aujourd'hui. Dans un grand nombre de cas, des géniteurs sauvages sont encore utilisés pour produire des juvéniles chez cette espèce, et l'on constate une forte prédominance des mâles, aux performances zootechniques inférieures, dans les populations d'élevage. Le but du présent travail de recherche était tout d'abord de quantifier les variations génétiques de la croissance et du sex ratio entre familles de bar produites par fécondation artificielle et élevées en commun, en utilisant le génotypage de locus microsatellites pour reconstruire les pedigrees des animaux mesurés. Dans un second temps, nous avons également étudié la réponse en termes de croissance et de sex ratio à une sélection expérimentale sur la croissance en longueur. Nous avons tout d'abord pu montrer que la technique expérimentale choisie (fécondation artificielle, élevage en commun et reconstruction des pedigrees par génotypage) était efficace et susceptible d'être appliquée non seulement en expérimentation, mais aussi pour la mise en place de programmes de sélection chez le bar. La croissance chez le bar montre une héritabilité élevée pour le poids à taille commerciale de 400g environ (h²=0.38-0.44), mais plus modeste pour le taux de croissance de 35 à 400g (0.16-0.34), montrant l'importance de la croissance précoce, très héritable (h²=0.61) dans la construction de la performance à taille commerciale. Par ailleurs, la croissance du bar n'est pas significativement influencée par des effets maternels non génétiques ou de dominance. Nous avons estimé les interactions génotype-milieu pour la croissance entre des sites de grossissement très différents, et si ces interactions se sont révélées modestes pour le poids à taille commerciale (rA=0.70-0.99 entre sites), elles étaient beaucoup plus fortes pour le taux de croissance (rA=0.21-0.61 entre sites). Bien que nous ayons à dessein choisi des environnements très différents pour ce test, ceci souligne l'importance de conduire les programmes de sélection dans un environnement proche de l'environnement d'élevage. Nous avons montré que le sex-ratio des populations naturelles de bar ne différait pas de 50-50 en moyenne, mais que certaines classes d'âge pouvaient avoir un sex-ratio biaisé, vraisemblablement du fait d'effets environnementaux. En élevage, les sex-ratios sont variables entre familles et influencés à la fois par le père et par la mère. Aucun modèle purement génétique ne permet d'expliquer les distributions observées, qui peuvent être décrites soit par un modèle ayant au moins deux loci bialléliques et une variance micro-environnementale, soit par un modèle polygénique à seuil (h²=0.62 pour la tendance sexuelle sur l'échelle sous-jacente). Avec ce dernier modèle, on note une corrélation génétique positive (rA=0.50) entre tendance sexuelle et croissance. Ceci permet de prédire que la domestication devrait permettre un rééquilibrage du sex-ratio vers 50-50, la sélection croissance biaisant le sex-ratio vers plus de femelles. C'est ce que nous observons ensuite dans notre expérience de réponse à la sélection pour la croissance. Cette même expérience nous permet de confirmer le potentiel de l'espèce pour une amélioration génétique de la croissance, avec un gain de 23% en première génération. Le modèle polygénique (ou à tout le moins polyfactoriel) de déterminisme du sexe est a priori rare chez les Vertébrés. Après avoir développé son utilisation possible pour obtenir à terme des populations de bars d'élevage monosexes femelles, le modèle polygénique est replacé dans la théorie du déterminisme du sexe chez les Vertébrés ectothermes, où il semble pouvoir être considéré comme beaucoup plus répandu qu'on ne le considère classiquement. [...] Suite et fin du résumé dans la thèse.

Made available in DSpace on 2014-06-11T19:26:06Z (GMT). No. of bitstreams: 0 Previous issue date: 2013-11-21Bitstream added on 2014-06-13T20:33:45Z : No. of bitstreams: 1 000749460.pdf: 1415671 bytes, checksum: 786699c8493a7bd8590e7f9c286f7c1f (MD5) / The aim of this study was to estimate genetic parameters between scrotal circumference obtained at 18 months of age (SC) and reproductive traits measured directly in Nellore females, such as number of calvings at 53 months (NC53), heifers rebreeding (HR) and stayability (STAY) in order to investigate the possibility of using traits measured directly in females as a selection criteria in cattle breeding programs, besides, studying and evaluating if number of calvings at 53 months could be used as an alternative way for measuring longevity in cattle herds. Two methods were applied for estimating variance components in order to predict breeding values: restricted maximum likelihood (REML) and Bayesian inference. The average estimates of heritability by bivariate model using REML were equal to 0.013 ± 0.003, 0.057 ± 0.007, 0.039 ± 0.007 and 0.530 ± 0.013 for NC53, STAY, HR and SC, respectively. Using the Bayesian method, the estimates were 0.22 ± 0.009, 0.19 ± 0.025, 0.15 ± 0.021 and 0.52 ± 0.019 for NC53, STAY, HR and SC, respectively. Based on the correlations between reproductive traits measured in females, the selection of animals for NC53 will cause anticipation on genetic evaluation of bulls for longevity, based on the performance of their daughters, from 76 to 53 months

Made available in DSpace on 2014-06-11T19:26:06Z (GMT). No. of bitstreams: 0 Previous issue date: 2013-09-04Bitstream added on 2014-06-13T20:14:39Z : No. of bitstreams: 1 000736074.pdf: 6614631 bytes, checksum: 30eeb90de773cb771d4462a991d2f8d8 (MD5) / Em razão da necessidade de produzir carne com qualidade, características de carcaça como a área de olho de lombo e a espessura de gordura subcutânea têm sido utilizadas como critérios de seleção de bovinos de corte. Ainda são poucos os estudos sobre essas características e suas associações com as características reprodutivas e de crescimento. O objetivo neste estudo foi estimar parâmetros genéticos para pesos ao nascer (PN), ao desmame (PD) e ao sobreano (PS), perímetros escrotais ao desmame (CED) e ao sobreano (CES), idade ao primeiro parto (IPP), área de olho de lombo (AOL) e espessura de gordura subcutânea (EG), em bovinos Canchim. Foram utilizadas 14.513 observações de animais da raça Canchim (5/8 Charolês + 3/8 Zebu) e do grupo genético MA (progênie de touro Charolês e vaca ½ Canchim + ½ Zebu) nascidos entre os anos de 1992 e 2012. As análises uni e bicaracterísticas foram realizadas utilizando inferência Bayesiana sob modelo animal que considerou como efeitos fixos o grupo de contemporâneos (sexo, fazenda, regime alimentar, grupo genético, estação e ano nascimento) e as covariáveis classe de idade da vaca ao parto e idade do animal na data da mensuração e como aleatórios, os efeitos genético aditivo direto e residual, sendo que para PN, PD e CED foi considerado, também, o efeito genético aditivo materno. As médias das estimativas de herdabilidade, obtidas pelas análises uni e bicaracterísticas, foram de 0,28; 0,30; 0,28; 0,33; 0,43; 0,15; 0,37 e 0,22 para PN, PD, PS, CED, CES, IPP, AOL e EG, respectivamente. As estimativas de herdabilidade sugerem que as características de crescimento e de carcaça, CED e CES devem responder a seleção direta. Correlações genéticas medianas e negativas sugerem que ganhos genéticos para redução de IPP podem ser obtidos ao selecionar animais para PS, CES e EG. Progressos genéticos podem ser alcançados nas... / Due to the demand for high quality meat, carcass traits such as loin eye area and backfat thickness have been used as criteria for beef cattle selection. Nevertheless, there is a lack of studies on these traits and on their association with the reproductive and growth traits commonly used in animal breeding program. The objective of this study was to estimate genetic parameters for birth (PN), weaning (PD) and long-yearling (PS) weights, scrotal circumference at weaning (CED) and long-yearling (CES), age at first calving (IPP), loin eye area (AOL) and backfat thickness (EG) in Canchim cattle. Data on 14,513 observations of Canchim (5/8 Charolais + 3/8 Zebu) and MA (offspring of Charolais bulls and ½ Canchim + ½ Zebu cows) animals, born between 1992 and 2012 were used. The analyses were carried out using Bayesian inference under an animal model that included the fixed effects of contemporary group (sex, farm, feeding regime, genetic group, season and year of birth) and covariates cow age class at calving and animal age at the measurement, besides the random, additive direct genetic and residual effects. For PN, PD and CED the maternal addictive effect was also considered in the model. The means of the heritability estimates obtained in one and two-trait analyses were 0.28, 0.30, 0.28, 0.33, 0.43, 0.15, 0.37 and 0.22 for PN, PD, PS, CED, CES, IPP, AOL and EG, respectively. The heritability estimates suggest that growth traits, carcass traits, and scrotal circumference at weaning and long-yearling should respond to direct selection. Moderate and negative genetic correlations suggest that reduction in IPP can be obtained by selecting animals for PS, CES and EG. Genetic progress can be achieved on carcass traits without causing losses to the reproductive and growth traits

Made available in DSpace on 2014-06-11T19:32:15Z (GMT). No. of bitstreams: 0 Previous issue date: 2013-07-05Bitstream added on 2014-06-13T19:42:43Z : No. of bitstreams: 1 000736349.pdf: 1557668 bytes, checksum: 5d8839f8bae5d3752139ce20dd197a5a (MD5) / A fauna de água doce no Brasil é particularmente diversa e muitas das espécies de peixes que a compõem não são encontradas naturalmente fora da América do Sul. Essa diversidade abrange um número elevado de estoques naturais, os quais vêm sofrendo sensível redução nos cursos d’água como resultado da exploração desordenada dos recursos. A piracanjuba (Brycon orbignyanus) é uma espécie do gênero Brycon de grande interesse econômico, seja pela apreciação de sua carne pelo mercado consumidor ou pelo seu comportamento agressivo quando capturado em pesca esportiva, o que lhe garante um alto valor comercial. Esta espécie está distribuída na bacia do rio Paraná, realiza migrações periódicas para reprodução e alimentação e está ameaçada de extinção, sendo que na última lista das espécies da fauna brasileira ameaçada de extinção, a piracanjuba foi classificada como criticamente em perigo. A variação genética dentro de uma espécie é um conceito fundamental para a genética aplicada à ecologia e diversos autores sugerem pelo menos três razões biológicas para a preservação da variabilidade genética das populações naturais como objetivos da biologia da conservação: a perda da variabilidade pode aumentar a probabilidade de extinção através de um declínio na fecundidade e viabilidade; populações com baixos níveis de variação genética, sobre as quais a seleção natural pode operar, podem ter oportunidades reduzidas para futuras adaptações frente a mudanças evolutivas; e a preservação da variabilidade genética pode ter papel chave na identificação de unidades evolutivas significativas para a formulação de programas de conservação. É neste contexto que este estudo realizou o estudo populacional da espécie Brycon orbignyanus, com a utilização de marcadores moleculares microssatélites e marcadores mitocondriais D-Loop, em exemplares capturados... / Not available

Made available in DSpace on 2015-06-17T19:33:48Z (GMT). No. of bitstreams: 0 Previous issue date: 2015-02-26. Added 1 bitstream(s) on 2015-06-18T12:48:02Z : No. of bitstreams: 1 000834150.pdf: 983221 bytes, checksum: 48c6e2b8c858629d2760705d7d88d3f8 (MD5) / O objetivo deste estudo foi estimar os componentes de variância para a característica aprumo em bovinos da raça Nelore, e realizar estudos de associação genômica ampla para identificar possíveis regiões genômicas relacionadas com sua expressão. Os registros de aprumo foram obtidos pela atribuição de escores visuais em dois momentos diferentes: FL1) característica binária medida ao sobreano, com o objetivo de identificar se o animal apresenta (FL1=1) ou não (FL1=0) defeito de aprumo; FL2) escores de aprumo variando de 1 (menos desejável) a 5 (mais desejável), foram designados aos animais top 20% para o índice de seleção adotado pelo programa de melhoramento genético de bovinos de corte PAINT (CRV Lagoa), e foram medidos em torno de 2 a 5 meses após a avaliação de sobreano. As características FL1 e FL2 foram avaliadas em conjunto com peso ao sobreano (YW). Os componentes de variância e covariância e os valores genéticos foram estimados por inferência Bayesiana, por meio de modelo animal bi-característica (três análises: FL1-FL2, YW-FL1 e YW-FL2). O estudo de associação genômica ampla (GWAS) para FL1 e FL2 foi realizado utilizando o método weighted single-step GBLUP, a partir do qual foram estimados os efeitos dos SNPs. As janelas top 10 de 1 Mb que explicam a maior proporção da variância genética foram observadas para cada característica. As médias (erros padrão) a posteriori das estimativas de herdabilidade foram iguais a 0,18 (0,04) e 0,39 (0,07), para FL1 e FL2, respectivamente. A estimativa de correlação genética entre FL1 e FL2 (-0,47) foi de moderada magnitude e negativa, conforme esperado, considerando que o escore de classificação que favorece cada característica corresponde a valores numéricos atribuídos em sentidos opostos. A correlação genética estimada entre FL2 e YW (0,39) sugere que a média do peso ao sobreano da população em estudo não é alta a ponto de causar ... / The aim of this study was to estimate variance components of two traits associated to feet and legs in Nelore cattle and identify putative genomic regions underlying the expression of these traits through genome-wide association (GWA) analyses. Feet and legs was evaluated by the assignment of visual scores at two different moments: FL1) binary trait measured at yearling (about 550 days of age), aimed to identify whether an animal had defects related to feet and legs (FL1=1) or not (FL1=0); FL2) feet and legs score ranging from 1 (less desirable) to 5 (more desirable) was assigned to the top 20% animals for the selection index adopted by the beef cattle breeding program PAINT (CRV Lagoa), which were measured around 2-5 months after the evaluation of yearling. The FL1 and FL2 traits were evaluated together with yearling weight (YW). The components of variance and covariance and breeding values were estimated by Bayesian inference, using two-trait animal models (three analyses: FL1-FL2, YW-FL1 and YW-FL2). The genome-wide association (GWA) analyses for FL1 and FL2 was performed using the weighted single-step GBLUP method, from which were estimated the SNP effects. Functional annotation was focused on the ten 1Mb windows explaining the largest fraction of the genetic variance for each trait. Posterior means (standard errors) of heritability estimates were equal to 0.18 (0.04) and 0.39 (0.07), for FL1 and FL2, respectively. The estimate of genetic correlation between FL1 and FL2 (-0.47) was of moderate magnitude and negative, as expected considering that the classification score that favors each trait represents numerical values assigned in opposite directions. The genetic correlation estimated between FL2 and YW (0.39) suggests that the average yearling weight of the studied population is currently not high enough to cause a negative association with feet and legs problems. The genetic trends estimated for FL1 and FL2 (-0.043 and ...

Le chien présente de nombreuses maladies génétiques dont les rétinopathies auxquelles je me suis intéressée. Historiquement, l’homme a appliqué aux chiens une sélection artificielle extrêmement forte, créant ainsi près de 400 races répondant à des besoins spécifiques. En uniformisant ainsi de nombreux traits phénotypiques et comportementaux, l’homme a sélectionné les allèles recherchés mais a également concentré involontairement des allèles délétères responsables de maladies génétiques. Ces maladies étant pour beaucoup cliniquement et génétiquement similaires aux maladies humaines, le chien constitue alors un modèle de choix pour en rechercher les bases génétiques et développer de nouvelles thérapies pour un bénéfice mutuel pour l’homme et le chien. J’ai travaillé sur l’Atrophie Progressive de la Rétine (APR) dans deux races avec le concours du Dr Gilles Chaudieu et des clubs de race : le border collie et le berger picard. Concernant l’APR du border collie, les analyses réalisées avant mon arrivée avaient identifié un locus de 20Mb sur le chromosome X. J’ai tout d’abord mis à jour les données épidémiologiques et cliniques d’environ 500 chiens et poursuivi la collecte de prélèvements. Une analyse de liaison génétique pangénomique sur 130 chiens m’a permis de confirmer le mode de transmission et le locus. J’ai ensuite conduis plusieurs analyses génétiques (« homozygosity mapping », analyses des génotypes, séquençage de gènes candidats) sans pour autant réduire le locus ni identifier de mutation causale. Dans ce contexte et grâce à l’avènement des nouvelles technologies de séquençage, j’ai choisi de séquencer le génome complet de trois chiens atteints et deux porteurs apparentés. Ce travail m’a permis d’identifier 117variants dont 9 dans le locus d’intérêt, mais aucun dans des régions codantes. Je me suis donc focalisée sur les variants de régions régulatrices pour 13 gènes candidats. De plus, j’ai identifié cinq variants structuraux, encore en cours d’étude. Concernant l’APR du berger picard, nous avons relancé le projet par la collecte de prélèvements et la réalisation d’un pedigree de 154 chiens. Ce travail a amené à une collaboration tripartite internationale par le séquençage de deux chiens atteints et deux indemnes d’APR, dont les analyses sont en cours. Cette thèse m’a permis d’aborder la génétique d’une maladie génétique rare chez l’homme grâce à un modèle spontané original ; et même si ce travail n’a pas abouti à l’identification de mutations à ce jour, ces APR restent de bons modèles génétique et thérapeutique pour les rétinites pigmentaires humaines. / Dogs are affected by numerous genetic diseases including retinopathies, the subject of my thesis. Historically, humans have exerted a very strong artificial selection to dogs, thus creating some 400 breeds to perform specific tasks or to harbour specific traits. By such an homogenisation of phenotypic and behavioural traits, humans have selected desired alleles but also concentrated undesired deleterious alleles responsible of genetic diseases. These diseases are clinically and genetically similar to human genetic diseases, making dogs a model of choice to search for the genetic bases of such genetic diseases and to develop new therapies for a mutual benefit for dogs and humans. I worked on Progressive Retinal Atrophies (PRA) in two breeds, thanks to the contribution of the veterinary ophthalmologist Dr. Gilles Chaudieu and the breed clubs of border collies and berger picard. Concerning the border collie PRA, genetic analyses performed before my thesis allowed the identification of a locus of 20Mb on the X chromosome. I first completed and supplemented the epidemiological and clinical data for about 500 dogs and continued the sample and data collection. A first genetic linkage analysis on 130 dogs allowed to confirm the transmission mode and the locus. I then performed several genetic analyses (« homozigosity mapping », genotypes analyses, candidate gene sequencing) without significantly reducing the locus,neither finding the causal mutation, unfortunately. In this context and thanks to the development of new sequencing technologies, I chose to sequence the entire genome of three PRA affected border collies and two unaffected related dogs. This work allowed the identification of 117variants, 9 in the locus but none in coding regions. I thus focused my research on genetic variants from potential regulatory regions for 13 candidate genes. In addition, I identified five structural variants. The analysis of these variants is still ongoing. Concerning the berger picard PRA, we have re-initiated the project by collecting samples and designing a large pedigree of 154 dogs. This workled to an international collaboration by the sequencing of the entire genomes of 2 affected and 2 unaffected bergers picards for which the statistical analyses are ongoing. This thesis allowed me to work on the genetics of rare diseases in humans with a spontaneous and original animal model and even if thiswork has not yet reached the identification of the mutations, these two PRAs in these two breeds remain good genetic and therapeutic models for human RP RetinitisPigmentosa.

Submitted by (edna.saturno@ufrpe.br) on 2017-04-10T13:19:21Z No. of bitstreams: 1 Elizabete Cristina da Silva.pdf: 4327297 bytes, checksum: 969fe0e6e726dc739f29566fd5377097 (MD5) / Made available in DSpace on 2017-04-10T13:19:21Z (GMT). No. of bitstreams: 1 Elizabete Cristina da Silva.pdf: 4327297 bytes, checksum: 969fe0e6e726dc739f29566fd5377097 (MD5) Previous issue date: 2010-08-12 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / In Brazil, naturalized pigs or animals called locally adapted are endangered species due to the overvaluation of exotic pig breeds that have caused loss of genetic diversity in these populations. Thus, this study aimed to characterize diversity and genetic structure of nine pig genetics groups locally adapted: Baé (n=11), Caruncho (n=07), Canastra (n=29), Canastrão (n=09), Mamelado (n=07), Moura (n=18), Nilo (n=16), Piau (n=17) and mongrel (SRD; n=47) and three exotic breeds (Duroc=04, Landrace=21 and Large White=04) with 18 microsatellite markers as well as testing these markers to allocate individuals from a mongrel population and their actual population. It was detected 198 alleles with 18 loci examined in 190 pigs from 12 genetic groups, all of them were polymorphic with PIC (polymorphic information content) ranged from 0.541 (SW72) to 0.933 (S0005). The results of AMOVA showed that 3.2% of total variation came from the difference between genetic groups (P<0.0001) and 3.6% (P<0.0001) between local and commercials pigs. The average alleles and alleles effectives Nea were lower for commercial Duroc breed (3.65 and 3.008) and higher for mongrel populations (8.89 and 4.53) and Canastra (8.61, 4.58) detaching the high genetic diversity of the last ones. The nine local GG showed greater average value for the rates: alleles average number (Nam = 7.22), Nea (4.18), PIC (0.67) and the expected heterozygosis (He = 0.71), while the heterozygosis observed (Ho = 0.60) was lower due to intrapopulation inbreeding (FIS = 0.17). Using the UPGMA method, Landrace breed was grouped with Canastra, Moura, Canastrão, Baé and Caruncho populations. Another group was formed by populations Piau, Mongrel, Nilo and Mamelado, while Large White and Duroc breeds were isolated from the rest. Based on the two populations (K=2) for allocation of mongrel pigs, most (71.8%) individuals SRD was grouped into separate clusters of commercial breeds. Two clusters seem to accordingly describe the distribution of genetic variability found in 12 GG, which showed low level of differentiation, leading to a complex population genetic structure and the 18 loci were effective to allocate mongrel individuals to their actual population. / No Brasil, os suínos naturalizados ou animais ditos localmente adaptados encontramse em via de extinção devido à supervalorização das raças suínas exóticas que tem ocasionado perda de diversidade genética nessas populações. Dessa forma, objetivou-se caracterizar a diversidade e estrutura genética de nove grupos genéticos (GG) de suínos localmente adaptados: Baé (n=11), Caruncho (n=07), Canastra (n=29), Canastrão (n=09), Mamelado (n=07), Moura (n=18), Nilo (n=16), Piau (n=17) e Sem Raça Definida (SRD; n=47) e três raças exóticas: Duroc (n=04), Landrace (n=21) e Large White (n=04) com 22 marcadores microssatélites, e testar a viabilidade desses marcadores para alocar indivíduos de um GG SRD à sua população real. Detectou-se 198 alelos com 18 loci analisados em 190 suínos de 12 GG, todos foram polimórficos com PIC (conteúdo de informação polimórfica) variando de 0,54 (SW72) a 0,93 (S0005). Os resultados da AMOVA mostraram que 3,2% da variação total foram provenientes da diferença entre GG (P<0,0001) e 3,6% (P<0,0001) entre suínos locais e comerciais. As médias de alelos totais e efetivo de alelo (Nea) foram menores para a raça comercial Duroc (3,65 e 3,01) e maiores para os GG SRD (8,89 e 4,53) e Canastra (8,61e 4,58). Os nove GG locais apresentaram maior valor médio para os índices: número médio de alelos (Nam = 7,22), Nea (4,18), PIC (0,67) e heterozigosidade esperada (He = 0,71), enquanto, a heterozigosidade observada (Ho = 0,60) foi menor devido à consanguinidade intrapopulacional (FIS = 0,17). Com exceção da raça Large White, todos os GG apresentaram desvio significativo (P<0,05) para o Equilíbrio de Hardy-Weinberg. Utilizando o método UPGMA a partir da distância genética padrão de Nei, a raça Landrace foi agrupada com os GG locais Canastra, Moura, Canastrão, Baé e Caruncho. Baseando-se nos dois grupamentos (K=2) para os testes de alocação dos suínos SRD, a maior parte (71,8%) dos indivíduos SRD foi agrupada em clusters separados das raças comerciais. Dois grupamentos parecem descrever adequadamente a distribuição da variabilidade genética encontrada nos 12 GG, os quais apresentaram baixo nível de diferenciação, conduzindo a uma estrutura genética populacional complexa, e os 18 loci foram eficazes para alocar os indivíduos SRD a sua população real.

Orientador: Vera Nisaka Solferini / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-13T04:40:21Z (GMT). No. of bitstreams: 1 Abreu_AluanaGoncalvesde_D.pdf: 3682927 bytes, checksum: e8b0e5d165148e225082c7057c66bb6e (MD5) Previous issue date: 2009 / Resumo: Tomoplagia reticulata (Diptera: Tephritidae) é um fitófago especialista em Eremanthus glomerulatus (Asteraceae). Os adultos ovipõem nas inflorescências da planta hospedeira, onde as larvas se desenvolvem. O histórico de coletas de T. reticulata mostra uma grande variação na quantidade de insetos infestando cada indivíduo de E. glomerulatus. A fim de verificar se a variação no número de herbívoros nas populações do hospedeiro é associada a alguma característica química e/ou genética deste, comparamos as variabilidades genética e química entre indivíduos de E. glomerulatus com diferentes níveis de infestação por T. reticulata (cap. 1). Eremanthus glomerulatus tem baixa variabilidade genética, provavelmente associada à distribuição restrita desta espécie. Apesar da distribuição fragmentada, há pouca estruturação entre as populações desta planta, explicada pelo maior fluxo gênico entre ambientes fragmentados em espécies anemocóricas. As características genéticas e químicas de E. glomerulatus não explicam a variação no nível de herbivoria das populações do hospedeiro. No capítulo 2, testamos a hipótese de que fitófagos especialistas apresentam maior diferenciação genética e menor diversidade do que generalistas, comparando o nível de variabilidade e estrutura genética de T. reticulata com o de outros fitófagos com diferentes amplitudes de hospedeiro. As populações de T. reticulata apresentaram baixa variabilidade e grande estruturação genética, o que é associado à distribuição fragmentada da planta hospedeira, que restringe a distribuição das pequenas populações do inseto. No capítulo 3, caracterizamos a composição genética das populações de Tomoplagia reticulata e de T. pallens, uma espécie irmã. Ambas as espécies parasitam E. glomerulatus; T. reticulata ocorre em MG e T. pallens em GO. Há uma zona de contato entre as espécies no Sul de MG, onde elas hibridizam. Ocasionalmente T. pallens chega ao centro de MG (Santana do Riacho), região mais fria. Esta migração provavelmente está associada a anos excepcionalmente quentes. / Abstract: Tomoplagia reticulata (Diptera: Tephritidae) is a phytophagous insect which is specialist on Eremanthus glomerulatus (Asteraceae). Adults oviposit in flower heads, where larvae develop. Sampling records for T. reticulata show that there is great variation in the number of insects parasitizing each plant. To verify if this variation is associated with chemical or genetic characteristics of the host plant, we assayed E. glomerulatus' genetic and chemical variability and compared between individuals with different levels of infestation by T. reticulata (chapter 1). Eremanthus glomerulatus has low genetic variability, probably related to its narrow geographic distribution. There is low genetic structure among populations despite its fragmented distribution, due to enhance gene flow in fragmented habitats in anemocoric species. E. glomerulatus' chemical and genetic characteristics don't explain variation in herbivory. In chapter 2, we tested the hypothesis that herbivorous insect species with narrow diet breadth are expected to be more prone to genetic differentiation and lower genetic diversity than insect species with a wider diet breadth, comparing T. reticulata's genetic variability and structure with other phytophagous with different host ranges. Tomoplagia reticulata has low genetic variability and great genetic structure, which is associated with its host fragmented distribution that restricts the distribution of insect populations. In chapter 3, we described genetic composition of Tomoplagia reticulata and T. pallens, a sister species. Both of them parasitize E. glomerulatus; T. reticulata occurs in MG and T. pallens in GO. There is a contact zone between them in southern MG, where they hybridize. Occasionally, T. pallens arrives in the center of MG (Santana do Riacho), a colder region. This migration is probably associated with extremely hot years. / Doutorado / Genetica Animal e Evolução / Doutor em Genetica e Biologia Molecular

Snappers of the genus Lutjanus are small to large predatory fishes occurring in inshore circumtropical and subtropical waters throughout the world. These fishes support fisheries across their distribution range. Within the Western Indian Ocean (WIO), previous studies on Lutjanus kasmira revealed limited spatial genetic differentiation, whereas Lutjanus fulviflamma showed high genetic connectivity. The phylogenetic relationships among WIO snappers are unknown. Previous studies in the Indo-Pacific (IP) did not include any WIO representatives. This study examined (1) the phylogeographic patterns in Lutjanus bohar, L. fulviflamma and L. lutjanus to understand the origins and factors influencing the distribution of diversity in the region, (2) how the physical environment, biological, and ecological factors influence genetic diversity, (3) the placement of WIO snappers in context to those from the IP, as well as the placement of taxa not included previously, (4) extent of differentiation among conspecifics from the two regions, and (5) the relationship of the Caesionidae to the Lutjanidae. Samples were sourced from across the WIO and from peripheral localities, where possible. DNA sequence data were generated from two mitochondrial gene regions (cyt-b and NADH-2) and a nuclear gene region (S7 intron 1). Data were analysed under a phylogeographic framework to examine genetic structure, diversity and differentiation among identified regions for each of the three species. Other sequence data were generated from two mitochondrial gene regions (COII and 16S rDNA) to examine the phylogenetic placement of WIO snappers in context of the IP snappers and the relationship of the Caesionidae to the Lutjanidae. Lutjanus bohar and L. fulviflamma displayed high genetic diversity, but lower diversities were observed for L. lutjanus. Genetic differentiation was observed between Mozambique and Maldives in L. bohar. Lutjanus fulviflamma was differentiated in South Africa, Mozambique, Mauritius and Thailand, while differentiation was observed between Kenya and Tanzania in Lutjanus lutjanus. Overall, low genetic differentiation and high connectivity were observed for each of the three species. This differentiation may result from intrinsic features of the species and extrinsic features of the environment, whereas the connectivity is mainly influenced by the pelagic larval duration. These patterns of differentiation are in accordance with a proposed vicariant biogeographic hypothesis for the origins of regional faunas of the IP. Phylogenies were similar to those published, with additional taxa not altering the previous groupings found. Conspecifics from the two regions clustered together, with varying degrees of differentiation among the WIO and IP, depending on the species. Members of the Caesionidae were nested within Lutjanidae, suggesting that morphological characters separating the two families are taxonomically insignificant. This affirms previous notions that the Caesionidae should be a subfamily within the Lutjanidae. This is the first multi-gene study, examining differentiation in multiple species of snapper over a wide geographic area in the WIO, and the results of this study could have potential implications for fisheries management and conservation.

L'espèce canine (Canis lupus familiaris) rassemble plus de 350 races issues d'une sélection artificielle drastique menée par l'Homme au cours des derniers siècles. De ce fait, chaque race peut être considérée comme un isolat génétique développant chacune des affections génétiques de manière spontanée avec parfois de fortes fréquences. Ainsi, l'espèce canine constitue un modèle puissant pour identifier les gènes et allèles responsables de ces affections homologues à certaines maladies génétiques humaines. Mon premier projet a porté sur la recherche des causes génétiques de deux kératodermies plantaires chez le terrier irlandais et le dogue de Bordeaux. En combinant plusieurs analyses d'association (GWAS : « Genome Wide Association Study ») et des techniques de séquençage NGS (Next Generation Sequencing), un nouveau gène muté a été identifié pour le terrier irlandais. Concernant les dogues de Bordeaux, nous avons génotypé plus de 170 000 SNPs sur plus de 200 dogues. Une analyse de liaison génétique a permis d'identifier un locus de 20 Mb sur le chromosome 9 contenant un cluster de kératines. En combinant les données cliniques et génétiques, la kératine 16 s'avérait le meilleur gène candidat. Son séquençage complet a permis d'identifier une mutation complexe générant une protéine tronquée. Des analyses de PCR quantitatives ont révélé que ce gène muté était sous exprimé chez les individus atteints. Ce travail nous permet donc de proposer cette race de chien comme le premier modèle animal spontané de kératodermie focale non-épidermolytique (FNEPPK). En parallèle de ce projet, j'ai mené des recherches sur les bases moléculaires d'un syndrome d'automutilation acrale décrit dans plusieurs races. Cette neuropathie est homologue aux neuropathies héréditaires sensitives et autonomes (HSANs) chez l'Homme et se caractérise par une perte de sensibilité à la douleur au niveau des membres. A partir d'un GWAS, j'ai pu identifier un locus de 1,5 Mb chez le chien, dont l'orthologue humain n'est pas encore décrit chez des patients HSANs. Le séquençage complet de ce locus a mené à l'identification d'un variant situé dans une région cis-enhancer en amont d'un gène candidat. La mise en évidence d'une sous-expression du gène candidat indique que ce variant régulateur semblerait modifier l'activité de l'enhancer nous permettant de le proposer comme la mutation causale chez le chien. Cette découverte offre donc de nouvelles perspectives de recherche pour des patients humains atteints de neuropathies héréditaires sensitives. En combinant des approches génétiques complémentaires sur des modèles spontanés de maladies bien caractérisées chez le chien, j'ai pu participer à l'identification de trois nouveaux gènes, dont deux excellents candidats pour ces maladies homologues humaines. Le troisième représente un vrai modèle spontané de kératodermie K16, ouvrant ainsi des perspectives thérapeutiques qui bénéficieront à l'Homme et au chien. / The dog species (Canis lupus familiaris) contains more than 350 distinct breeds resulting from human drastic selection during the last centuries. Each breed can then be considered as a genetic isolate, developing specific spontaneous genetic diseases with high frequencies. Thus, dogs constitute a powerful model to identify new genes and alleles involved in disorders homologous to human diseases. For my thesis, I worked on two main topics. The first one focused on the search of the genetic causes of two footpad keratodermas in the Irish terrier and the dogue de Bordeaux breeds. Concerning the Irish terrier, the work was conduced by Tosso Leeb’s team in the University of Berne, in collaboration with the Antagene Company. Using a Genome Wide Association Study (GWAS) and Next Generation Sequencing (NGS), the mutation in a new gene has been identified in footpad hyperkeratosis in this breed. For the dogue de Bordeaux project, we genotyped more than 170 000 SNPs on over 200 dogs. We then performed a genetic linkage study with a subset of 68 dogs, including 14 affected dogs. We identified a significant locus of 20 Mb on the canine chromosome 9 containing one keratin cluster. Comparing clinical, histopathological and immunochemistry data, keratin 16 appeared as an excellent candidate. The sequencing of the gene revealed a complex mutation leading to a non-functional truncated K16 protein. Quantitative RT-PCR analyses showed a strong decrease of the level of KRT16 expression in affected footpads. These results led to propose the dogue de Bordeaux footpad hyperkeratosis as the first spontaneous model of focal non-epidermolytic palmoplantar keratoderma (FNEPPK). In parallel, I studied an acral mutilation syndrome described in several hunting dog breeds. This neuropathy corresponds to human hereditary sensory and autonomic neuropathies (HSANs) and is characterized by an insensitivity to pain only in the limb. With a classical GWAS strategy, using 24 affected and 30 unaffected dogs, we identified a 1.5 Mb locus in dogs, the human orthologous locus being still unknown in human patients. Targeted sequencing of this locus revealed one single variant localized in a cis-enhancer region closed to a strong candidate gene. A lower level of expression of the candidate gene in affected dogs seems to show a functional effect of the mutation in the enhancer activity. These results led to propose this variant as the causative mutation for this canine neuropathy, and so this canine model as an opportunity to identify a new human HSAN gene. Combining complementary genetic approaches on spontaneous models of well characterized canine diseases, I did participated to the identification of three new genes, two of which being novel excellent candidates for the homologous human diseases. The third represents a true homologous model of KRT16 human keratoderma, opening the field to the development of new treatments benefiting to both humans and dogs.