Gene expression responds to the environment and can also evolve rapidly in response to altered selection regimes. Little is known, however, about the extent to which evolutionary adaptation to a particular type of stress involves changes in the within-generation ('plastic') responses of gene expression to the stress. We used microarrays to quantify gene expression plasticity in response to ethanol in laboratory populations of Drosophila melanogaster differing in their history of ethanol exposure. Two populations ('R' populations) were maintained on regular medium, two ('E') were maintained on medium supplemented with ethanol, and two ('M') were maintained in a mixed regime in which half of the population was reared on one medium type, and half on the other, each generation. After more than 300 generations, embryos from each population were collected and exposed to either ethanol or water as a control, and RNA was extracted from the larvae shortly after hatching. Nearly 2000 transcripts showed significant within-generation responses to ethanol exposure. Evolutionary history also affected gene expression: the E and M populations were largely indistinguishable in expression, but differed significantly in expression from the R populations for over 100 transcripts, the majority of which did not show plastic responses. Notably, in no case was the interaction between selection regime and ethanol exposure significant after controlling for multiple comparisons, indicating that adaptation to ethanol in the E and M populations did not involve substantial changes in gene expression plasticity. The results give evidence that expression plasticity evolves considerably more slowly than mean expression.

This dissertation involved two experiments, (1) the study of realized heritabilities of correlated traits, and (2) the study of the inheritance of sexual dimorphism or body weight. The first experiment included data from four generations of double two-way selection for body weight and breast angle at eight weeks of age. Breast angle was considered a correlated trait in the weight subpopulation and body weight a correlated trait in the angle subpopulation. There was a significant divergence between lines for both selected traits. The response to direct selection for breast angle was asymmetrical with the response in the narrow direction being greater then that in the broad direction. The response of body weight to two-way selection was symmetrical through the F₄ generation. Divergence of body weight between the lines selected for breast angle was significant in the F₁, F₃, and F₄ generations. Divergence of breast angle between the lines selected for body weight was significant in the F₂ and subsequent generations. Heritabilities of the unselected traits were obtained by the cumulative difference between lines divided by the expected secondary selection differential and by the regression of the cumulative difference between lines on expected secondary selection differential. The correlated realized heritability of breast angle was greater in the weight lines than was the correlated realized heritability for body weight in the angle lines. Examination of the components of the correlated realized heritability showed that they were the ratio of the genetic to phenotypic covariances of the two traits. The second experiment involved the investigation of sex dimorphism for body weight at eight weeks of age. The heritability estimate for sex dimorphism of this trait was .02, and the genetic correlation of it in males and females was .98. The genetic variability (.02) in sex dimorphism was evidenced by a greater response in males to selection for eight-week body weight than in females. The biological reason for this was additive sex-linkage. / Ph. D.

Sexual differences are dramatic and widespread across taxa. However, a common genome between males and females should hinder phenotypic divergence. In this thesis I have used experimental, genomic, and theoretical approaches to study processes that can facilitate and maintain differences between males and females. I studied two mechanisms for the evolution of sexual dimorphism - condition-dependence and gene duplication. If sex-specific traits are costly, then individuals should only express such traits when they possess enough resources to do so. I experimentally manipulated adult condition and found that the sex-biased gene expression depends on condition. Second, duplication events can permit different gene copies to adopt sex-specific expression. I showed that half of all duplicate families have paralogs with different sex-biased expression patterns between members. I investigated how current sexual dimorphism may support novel dimorphism. With regards gene duplication, I found that related duplicates did not always have different expression patterns. However, duplicating a pre-existing sex-biased gene effectively increases organismal sexual dimorphism overall. From a theoretical perspective, I investigated how sexually dimorphic recombination rates allow novel sexually antagonistic variation to invade. Male and female recombination rates separately affect invasion probabilities of new alleles. Finally, I examined the assumption that a common genetic architecture impedes the evolution of sexual dimorphism. First, I conducted a literature review to test whether additive genetic variances in shared traits were different between the sexes. There were few significant statistical differences. However, extreme male-biased variances were more common than extreme female-biased variances. Sexual dimorphism is expected to evolve easily in such traits. Second, I compared these results to findings from the multivariate literature. In contrast to single trait studies, almost all multivariate studies of sexual dimorphism have found variance differences, both in magnitude and orientation, between males and females. Overall, this thesis concludes that sexual dimorphism can evolve by processes that generate novel sexual dimorphism or that take advantage of pre-existing dimorphism. Furthermore, a common genome is not necessarily a strong barrier if genetic variances differ between the sexes. It will be an exciting challenge to understand how mutation and selection work together to allow organisms differ in their ability evolve sexual dimorphism.

Sexual differences are dramatic and widespread across taxa. However, a common genome between males and females should hinder phenotypic divergence. In this thesis I have used experimental, genomic, and theoretical approaches to study processes that can facilitate and maintain differences between males and females. I studied two mechanisms for the evolution of sexual dimorphism - condition-dependence and gene duplication. If sex-specific traits are costly, then individuals should only express such traits when they possess enough resources to do so. I experimentally manipulated adult condition and found that the sex-biased gene expression depends on condition. Second, duplication events can permit different gene copies to adopt sex-specific expression. I showed that half of all duplicate families have paralogs with different sex-biased expression patterns between members. I investigated how current sexual dimorphism may support novel dimorphism. With regards gene duplication, I found that related duplicates did not always have different expression patterns. However, duplicating a pre-existing sex-biased gene effectively increases organismal sexual dimorphism overall. From a theoretical perspective, I investigated how sexually dimorphic recombination rates allow novel sexually antagonistic variation to invade. Male and female recombination rates separately affect invasion probabilities of new alleles. Finally, I examined the assumption that a common genetic architecture impedes the evolution of sexual dimorphism. First, I conducted a literature review to test whether additive genetic variances in shared traits were different between the sexes. There were few significant statistical differences. However, extreme male-biased variances were more common than extreme female-biased variances. Sexual dimorphism is expected to evolve easily in such traits. Second, I compared these results to findings from the multivariate literature. In contrast to single trait studies, almost all multivariate studies of sexual dimorphism have found variance differences, both in magnitude and orientation, between males and females. Overall, this thesis concludes that sexual dimorphism can evolve by processes that generate novel sexual dimorphism or that take advantage of pre-existing dimorphism. Furthermore, a common genome is not necessarily a strong barrier if genetic variances differ between the sexes. It will be an exciting challenge to understand how mutation and selection work together to allow organisms differ in their ability evolve sexual dimorphism.

Diss. (sammanfattning) Uppsala : Sveriges lantbruksuniversitet, 2005. / Härtill 5 uppsatser.

Made available in DSpace on 2014-06-11T19:26:06Z (GMT). No. of bitstreams: 0 Previous issue date: 2011-07-27Bitstream added on 2014-06-13T19:54:01Z : No. of bitstreams: 1 irano_n_me_jabo.pdf: 187304 bytes, checksum: 9f2cf22f2fa39eab86ecdfc75843adfe (MD5) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Objetivou-se com este trabalho estimar parâmetros genéticos para produção de leite, habilidade de permanência da vaca no rebanho e ocorrência de mastite clínica de vacas da raça Holandesa, bem como estudar as associações genéticas entre elas, com intuito de fornecer subsídios para a avaliação genética destas características. Foram analisados dados de 5.090 vacas da raça Holandesa que pariram no período de 1991 a 2010, pertencentes à Agropecuária Agrindus S.A.. Foram feitas duas análises multicaracterísticas, uma contendo as características produção de leite acumulada até 305 dias na primeira lactação (PL1), habilidade de permanência das vacas no rebanho (HP) até a terceira lactação e ocorrência de mastite clínica (OM) e, a outra, produção de leite acumulada até 305 dias (P305), HP e OM, ambas sob modelos animal e considerando as três primeiras lactações como medidas repetidas para P305 e OM. Os componentes de covariância foram obtidos por abordagem Bayesiana, utilizando o programa THRGIBBS1F90. As estimativas de herdabilidade, obtidas pela análise multicaracterísticas com a PL1, foram de 0,19; 0,28 e 0,13 para a PL1, HP e OM, respectivamente, enquanto que, na análise multicaracterísticas com a P305, as estimativas foram de 0,19; 0,31 e 0,14, respectivamente. As correlações genéticas foram de 0,38 entre PL1 e HP, 0,12 entre PL1 e OM e -0,49 entre HP e OM, em análise multicaracterísticas com a PL1 e, de 0,66 entre P305 e HP, -0,25 entre P305 e OM e - 0,52 entre HP e OM, em análise multicaracterísticas com a P305 / The objective of this study was to estimate genetic parameters for milk yield, stayability and the occurrence of clinical mastitis in Holstein cows, as well as studying the genetic relationship between them, in order to provide subsidies for the genetic evaluation these traits. Records from 5,090 Holstein cows with calving varying from 1991 to 2010, belonging to the Agropecuária Agrindus S.A. Two standard multivariate analyses were carried out, one containing the trait of accumulated 305 day milk yields in first lactation (MY1), stayability (SA) to the third lactation and clinical mastitis (CM) and the other, accumulated 305 day milk yields (MY), SA and CM, considering the first three lactations as repeated measures for MY and CM. The covariance components were obtained by Bayesian approach using the program THRGIBBS1F90. The heritability estimates obtained by multivariate analysis with MY1, were 0.19, 0.28 and 0.13 for MY1, SA and CM, respectively, whereas the multivariate analysis with the MY, the estimates were 0.19, 0.31 and 0.14, respectively. The genetic correlations between MY1 and SA, MY1 and CM, SA and CM, respectively, were 0.38, 0.12, and -0.49. The genetic correlations between MY and SA, MY and CM, SA and CM, respectively, were 0.66, -0.25, and -0.52

Resumo: Objetivou-se com este trabalho estimar parâmetros genéticos para produção de leite, habilidade de permanência da vaca no rebanho e ocorrência de mastite clínica de vacas da raça Holandesa, bem como estudar as associações genéticas entre elas, com intuito de fornecer subsídios para a avaliação genética destas características. Foram analisados dados de 5.090 vacas da raça Holandesa que pariram no período de 1991 a 2010, pertencentes à Agropecuária Agrindus S.A.. Foram feitas duas análises multicaracterísticas, uma contendo as características produção de leite acumulada até 305 dias na primeira lactação (PL1), habilidade de permanência das vacas no rebanho (HP) até a terceira lactação e ocorrência de mastite clínica (OM) e, a outra, produção de leite acumulada até 305 dias (P305), HP e OM, ambas sob modelos animal e considerando as três primeiras lactações como medidas repetidas para P305 e OM. Os componentes de covariância foram obtidos por abordagem Bayesiana, utilizando o programa THRGIBBS1F90. As estimativas de herdabilidade, obtidas pela análise multicaracterísticas com a PL1, foram de 0,19; 0,28 e 0,13 para a PL1, HP e OM, respectivamente, enquanto que, na análise multicaracterísticas com a P305, as estimativas foram de 0,19; 0,31 e 0,14, respectivamente. As correlações genéticas foram de 0,38 entre PL1 e HP, 0,12 entre PL1 e OM e -0,49 entre HP e OM, em análise multicaracterísticas com a PL1 e, de 0,66 entre P305 e HP, -0,25 entre P305 e OM e - 0,52 entre HP e OM, em análise multicaracterísticas com a P305 / Abstract: The objective of this study was to estimate genetic parameters for milk yield, stayability and the occurrence of clinical mastitis in Holstein cows, as well as studying the genetic relationship between them, in order to provide subsidies for the genetic evaluation these traits. Records from 5,090 Holstein cows with calving varying from 1991 to 2010, belonging to the Agropecuária Agrindus S.A. Two standard multivariate analyses were carried out, one containing the trait of accumulated 305 day milk yields in first lactation (MY1), stayability (SA) to the third lactation and clinical mastitis (CM) and the other, accumulated 305 day milk yields (MY), SA and CM, considering the first three lactations as repeated measures for MY and CM. The covariance components were obtained by Bayesian approach using the program THRGIBBS1F90. The heritability estimates obtained by multivariate analysis with MY1, were 0.19, 0.28 and 0.13 for MY1, SA and CM, respectively, whereas the multivariate analysis with the MY, the estimates were 0.19, 0.31 and 0.14, respectively. The genetic correlations between MY1 and SA, MY1 and CM, SA and CM, respectively, were 0.38, 0.12, and -0.49. The genetic correlations between MY and SA, MY and CM, SA and CM, respectively, were 0.66, -0.25, and -0.52 / Orientador: Lucia Galvão de Albuquerque / Coorientador: Annaiza Braga Bignardi / Coorientador: Lenira El Faro / Banca: Vera Lucia Cardoso / Banca: Humberto Tonhati / Mestre

Les apports de l’aquaculture représentent aujourd’hui la moitié des produits aquatiques destinés à la consommation humaine. La composition de l’aliment artificiel utilisé en élevage piscicole a fortement évolué ces 30 dernières années. Les produits d’origine végétale terrestre y ont progressivement remplacé les farines et les huiles de poisson lorsque les stocks de pêche minotière utilisés pour leur production se sont rapprochés de leur limite d’exploitation. Toutefois, l’usage exclusif de ces farines et huiles végétales conduit encore à la dégradation de la croissance et de la santé des salmonidés et des poissons marins. Dans le même temps, l’amélioration génétique en pisciculture a permis, depuis 1980, des gains importants sur les caractères de croissance, de santé et de qualité et dispose aujourd’hui de méthodes pour étudier les conséquences de cette profonde transition alimentaire sur les populations actuelles et futures issues des programmes de sélection. En privilégiant la comparaison entre un aliment composé de produits d’origine marine (M) et un aliment entièrement constitué de produits d’origine végétale terrestre (PB), nous avons étudié les voies d’amélioration génétique chez deux espèces majeures du secteur français : le bar européen (Dicentrarchus labrax) et la truite arc-en-ciel (Oncorhynchus mykiss). Dans ce contexte, l’objectif était en particulier d’estimer les héritabilités des caractères d’intérêt et l’importance des interactions génotype-aliment, qui sont à l’origine de reclassement des génotypes en fonction l’aliment utilisé.Les essais réalisés ont confirmés l’effet de la substitution totale sur la croissance et la composition lipidique chez les deux espèces et sur la survie chez le bar. Les héritabilités estimées des poissons nourris avec l’aliment PB pour le poids, la croissance et les paramètres de transformation technologique (rendement carcasse, viscères, tête, filet) sont hautes chez la truite (respectivement 0,69 ; 0,65 ; 0,21-0,58) et modérées chez le bar (respectivement 0,18 et 0,11). Pour ces caractères, les interactions génotype-aliment sont modérées et les corrélations génétiques estimées entre les aliments M et PB sont élevées chez la truite (respectivement 0,90 ; 0,92 ; 0,65-0,96) et chez le bar (respectivement 0,96 ; 0,64). Les gains génétique attendus sont plus élevés avec l’aliment PB qu’avec l’aliment M chez la truite tandis qu’ils sont plus faible chez le bar. La mesure de la réponse à la sélection pour une aptitude à grandir et à survivre en utilisant l’aliment PB a confirmé des gains élevés pour le poids (+35%), la survie (+15,1%) et la biomasse produite (+54,4%) sans impact sur les paramètres de transformation technologique (carcasse, viscères, tête, filet). Les essais réalisés ont confirmé que cette meilleure aptitude était liée à des modifications de l’activité du métabolisme lipidique mais n’ont pas permis de conclure à des liens avec l’ingéré et efficacité alimentaire.Les plus fortes mortalités et le plus faible poids des lots PB durant les jours qui suivent les premières prises alimentaires ainsi que les reclassements familiaux plus importants en début de cycle de vie indiquent que les stades précoces ont une place prépondérante dans l’utilisation de l’aliment d’origine végétale aux niveaux phénotypique et génétique et devront être approfondis.A la vue des résultats obtenus, il semble donc possible d’exploiter la grande plasticité de certaines espèces de poissons pour concevoir des programmes de sélection prenant en compte l’évolution des environnements de production. La limitation mondiale des ressources alimentaire confronte les élevages à des modifications rapides de l’aliment et l’amélioration génétique des cheptels peut aider à faciliter ces transitions alimentaires. / Nowadays, aquaculture contributes to half of the aquatic products intended for human consumption. The composition of aquafeeds strongly evolved in the past 30 years. Terrestrial plant-based products gradually replace fish meal and fish oil, as fish stocks used for their production reach their exploitation limit. However, the use of diets containing vegetable oils and meals only still lead to growth and health degradation in salmonids and marine fish.Besides, breeding programmes in fish farming allowed strong genetic progress, since 1980, on growth, health and quality traits. An important issue for fish breeders is now to understand the consequences of this deep dietary change on the current and future selected populations and to adapt breeding programs accordingly.Focusing on the comparison between two experimental diets, a diet containing marine products (M) and a diet containing only plant-based products, (PB), we investigated the possible impact of the dietary changes on the organization and the objectives of breeding programs in two major species of the French sector: the European sea bass (Dicentrarchus labrax) and the rainbow trout (Oncorhynchus mykiss). A key objective was to estimate the heritabilities of the main traits of economic interest and the importance of genotype by diet interactions, which may cause genotypes rerankings according to diet used. We also sought the potential origin of the variability for ability to use the PB diet and proposed scenarii for evolution of breeding programs.The trials confirmed that substitution of marine ingredients by vegetal ones decreased growth and lipid composition in both species, as well as survival in sea bass and, to a lesser extent in rainbow trout. The estimates of heritabilities for weight, growth and processing traits (carcass viscera, head and filet yields only measured on trout) when fish were fed with the PB diet were high in rainbow trout (respectively 0.69; 0.65; 0.21-0.58) and weak in sea bass (respectively 0.18 and 0.11). In trout and sea bass, these estimates were respectively higher and lower than those obtained when fish were fed the M diet. For these traits, genotype by diet interactions were moderate and the genetic correlations between the M and PB diets were variable in trout (respectively 0.67-0.90; 0.92; 0.65-0.96) and sea bass (respectively 0.51-0.96; 0.64) but could involve important family rerankings according to the period of survey. According to heritability estimates, expected genetic gains would be higher in trout for fish fed the PB diet than for fish fed the M diet when they would be weaker in sea bass. In trout, the measurement of the response to one generation of selection for the ability to grow and survive when fed the PB diet confirmed the results, and provided high genetic gains for body weight (+35%), survival rate (+15,1%) and produced biomass (+ 54,4%) without any impact on the processing traits (carcass, viscera, head, filet). We showed that this ability was associated to modifications in the lipid metabolism activities but could not establish links with feed intake or feed efficiency from our trials. Higher mortality rate and lower body weight in the PB batches during the first days following distribution of PB diet as well as stronger family rerankings in early steps of the survey indicate than the early stages play a key role in the use of plant-based diet at both phenotypic and genetic levels. Further insights dedicated to these particular stages are strongly needed.Based on present results, it seems possible to exploit the great plasticity of some fish species to conceive breeding programs taking into account a changing dietary environment. Facing the world limitation in food resources, genetic improvement of fish livestock can be a useful lever to facilitate dietary transitions.

A realização deste estudo teve como objetivo a estimação de componentes de (co) variância e parâmetros genéticos das características: peso (PES18), perímetro escrotal (PE18), precocidade de acabamento (PREC), musculosidade (MUSC) e altura (ALT), mensuradas aos 18 meses de idade, ganho de peso da desmama ao sobreano (GP345) e idade ao primeiro parto (IPP) de bovinos Nelore, utilizando-se modelos multicaracterísticas. Foram avaliados dados de 107.332 mil bovinos criados entre os anos de 1994 e 2009 em fazendas localizadas nos estados de São Paulo, Mato Grosso do Sul e Goiás, e pertencentes ao Programa de Seleção da raça Nelore da Agropecuária CFM Ltda. Utilizaram-se três diferentes modelos: modelo multicaracterísticas padrão, modelo de componentes principais e de análise de fatores, esses dois últimos contemplando os três primeiros componentes e fatores, os quais foram comparados por critérios de informação de Akaike (AIC) e Bayesiano de Schwarz (BIC). O modelo que utilizou a técnica da análise de fatores contemplando os dois primeiros fatores (MFA2) apresentou melhor ajuste, seguido do modelo que contemplou os 3 primeiros fatores (MFA3). Estes possibilitaram estimativas próximas das realizadas pelos modelos multicaracterísticas padrão, às quais se mostraram parecidas com os valores já relatados e estimados no Brasil. / This study was objectified the estimation of (co)variance components and genetics parameters of traits: weight (W18), scrotal circumference (SC18), precocity finishing (PREC), muscularity (MUSC) and height (H), measured at 18 months of age, weight gain from weaning to yearling (WG345) and age at first calving (AFC) from Nellore cattle, using multi trait models, with analysis multi trait standard, analysis of principal components and factor analysis. Were evaluated data from 107,332 bovines, managed between the years of 1994 and 2009 in farms localized on states of São Paulo, Mato Grosso do Sul and Goias, and were participants in Nellore Selection Program from CFM Company Ltda. Was utilized three different models, multi trait model, model of principal components and factor analytic, these two last contemplating the four first principal components and factors analytics and that was compared by information criteria of Akaike (AIC) and Bayesian of Schwarz (BIC). The model that used the factor analysis technique contemplating the first two factors (MFA2) presented better adjustment, followed by the model that contemplated the first 3 factors (MFA3). These allowed close estimates to those performed by the standard multi trait models, which were similar to the values already reported and estimated in Brazil.

Com as constantes mudanças do sistema produtivo de bovinos de corte, e um mercado consumidor ainda mais exigente, o enfoque sobre a escolha de animais que apresentem qualidade e rendimento de carcaça é cada vez maior. Para que as reivindicações dos frigoríficos sejam atendidas, o criador necessita de ferramentas de avaliação genética que possam identificar com mais precisão os touros que serão, de fato, melhoradores para as características desejáveis. Com isso, este trabalho teve como objetivo: (i) Estimar os componentes de variância e covariância, e os parâmetros genéticos para a característica de musculosidade em animais da raça Nelore; (ii) Estimar os componentes de variância e covariância, e os parâmetros genéticos para características de desenvolvimento ponderal (peso ao nascimento, peso a desmama, ganho de peso aos 345 dias) e reprodutivo (circunferência escrotal) em animais da raça Nelore; (iii) Estimar a correlação entre as características de musculosidade, desenvolvimento ponderal e reprodutivo; (iv) Comparar as metodologias que consideram o grupo de manejo a desmama como efeito fixo e aleatório; (v) Comparar as metodologias uni, bi e multicaracterística e avaliar as vantagens em incluir nos programas de seleção, através do cálculo de resposta correlacionada, a característica de musculosidade; (vi) Estimar as DEP´s para as características de musculosidade, desenvolvimento ponderal e reprodutivo; (vii) Comparar as metodologias multicaracterística e bivariadas na avaliação genética de touros, através do cálculo de perda de eficiência de seleção. / With the constant changes in the beef cattle production system, and an even more demanding consumer market, the focus on the carcass yield and quality is increasing. For the slaughters claims to be met, the breeder needs a tool that can identify the bulls that will be, in fact, the improvers to those specific features. Therefore, this project aims to: (i) Estimate the variance and covariance components, and the genetic parameters for the muscle score trait in Nellore animals; (ii) Estimate the variance and covariance components, and the genetic parameters for the growth traits (birth weight, weaning weight, post-weaning gain) and reproductive traits (scrotal circumference) in Nellore animals; (iii) Estimate the correlation between muscle score, growth and reproductive traits; (iv) Compare methodologies that consider the weaning management group as fixed and random effects; (v) Compare uni, bi and multi-trait methodologies and evaluate the advantages to include in the animal breeding programs, by the correlated response, the muscle score trait; (vi) Estimate the EPD\'s for muscle score, growth and reproductive traits and (vii) Compare the multi-trait and bivariate methodologies in the genetic evaluation of bulls through the calculation of selection efficiency loss.