Jatropha curcas L., também conhecida no Brasil como pinhão-manso, é uma oleaginosa que atraiu a atenção do mundo para bioenergia dado a qualidade e o alto conteúdo de óleo na semente. Contudo, a espécie necessita de programas de melhoramento genético para fixar características de interesse em bancos de germoplasma. Este trabalho objetivou identificar e analisar a diversidade alélica, metabólica e físico-química relacionada à síntese de óleo e ésteres de forbol em uma amostra de 22 genótipos do BAG do Instituto Agronômico de Campinas para seleção de genótipos elite. Os genes MFP2, KASIII e 3-N-D, envolvidos na biossíntese de óleo e de taxol, foram selecionados a partir de Gomes et al. (2010). Os resultados mostraram que há baixa diversidade alélica para os genes KAS III e MFP2, por outro lado, a expressão desses mesmos genes e a composição de ácidos graxos foi bastante variável entre os genótipos e ao longo do desenvolvimento da semente de J. curcas indicando uma provável regulação diferenciada da via de óleo. O estudo realizado permite combinar a diversidade alélica, expressão dos genes, conteúdo metabólico e poder calorífico para a seleção de genótipos e identificação de parentais direcionando cruzamentos no quadro do programa de melhoramento do IAC. / Jatropha curcas L., also know in Brazil as physic nut, is an oilseed that call world´s attention to bioenergy due to quality and high oilseed content. However, this species needs of breeding programs so that interest traits may to be fixed in germplasm banks. This study aimed to identify and analyze allelic, metabolic and physicochemical diversity related to oil and phorbol esters synthesis in a 22 genotypes sample from Instituto Agronômico de Campinas-BAG for elite genotypes selection. The MFP2, KASIII and 3-ND genes involved in oil and taxol biosynthesis were selected from Gomes et al. (2010). The results showed that there is low allelic diversity for KAS III and MFP2 genes, on the other hand, the expression of these same genes and fatty acid composition was quite variable between genotypes through J. curcas seed development indicating a putative differential regulation in oil pathway. This study allows combining allelic diversity, gene expression, metabolic content and calorific values for parental genotypes identification and selection driving crosses within IAC breeding program.

Aquaculture plays an important role in economic development and food security in many countries in the world. World aquaculture production in 2006 was 51.7 million tonnes with an estimated value of US$ 78.8 billion (FAO, 2009). World production will need to increase however by 30-40 million tonnes from its current production level by 2030 to meet growing global demand for fish. In this context, aquaculture in Vietnam has developed rapidly over the past decade and the fisheries sector ranked fourth in terms of export value in 2008 (Vietnamnet, 2008). Total fisheries production in Vietnam in 2007 was 4.149 million tonnes, of which fisheries production from catch and aquaculture were 2.064 and 2.085 million tonnes, respectively. A variety of aquatic species are cultured in Vietnam, but shrimps (mainly Black Tiger shrimp Penaeus monodon, and Pacific white shrimp Litopenaeus vannamei) and ‘tra’ or ‘basa’ catfish are the most common species used in aquaculture. The giant freshwater prawn (GFP), Macrobrachium rosenbergii, is one of the most important crustacean species in inland aquaculture in many countries across the world where this species is either native or exotic. GFP is suitable for culture in a variety of farming systems, including monoculture or polyculture in ponds, pens, and integrated or rotational rice-prawn culture models. The GFP industry worldwide relies totally on wild or unimproved stocks, a practice that threatens the long-term sustainability of GFP farming due to low productivity and vulnerability of farmed stocks to disease. The current status of GFP aquaculture highlights the need for initiation of a systematic stock improvement program for the species to improve economically important traits. Large-scale selective breeding programs have been instigated for some finfish, salmonids and GIFT tilapia for example, and some selective breeding trials have been conducted on crustacean species, namely marine penaeid shrimp and freshwater crayfish. Examples of selective breeding programs on aquatic species have demonstrated that significant genetic gains can be achieved for growth rates with gains of around 10-20% per generation. While a selective breeding program is an option for GFP stock improvement, an alternative approach to improving GFP productivity, potentially with more immediate effect and one that is less expensive, is crossbreeding which may produce heterosis or hybrid vigour in crossbred offspring. Therefore, a crossbreeding strategy was trialed in the current study as a starting point for a stock improvement program for the GFP industry in Vietnam. The current study assessed the growth performance of three GFP strains (two wild Vietnamese strains from the Dong Nai and Mekong rivers, and a single domesticated Hawaiian strain) and their reciprocal crosses in a complete 3x3 diallel cross, i.e. three purebred and six crossbred strains. The diallel cross was carried out over two consecutive generations (G1 and G2). Juveniles for the experiments were produced using single-pair matings. Juveniles from each strain combination were stocked into three replicate hapas for 15 weeks. Growth data (body weight, carapace length, standard length) from the G1 and G2 were pooled for all subsequent analyses as there was no effect of generation on growth traits. Results showed that the Hawaiian strain performed best among purebred strains, and crosses with the Dong Nai or Mekong strains as dams and the Hawaiian strain as sires grew significantly faster than did the purebred Dong Nai or Mekong strains. These results suggest potential for heterosis among some crosses. Growth data were analyzed in depth by partitioning the strain combination (cross) effect into three components: strain additive genetic effects, heterotic effects, and strain reciprocal effects. Strain additive genetic and reciprocal effects were significant sources of variation for all growth traits measured. Strain additive genetic effects were highest for the Hawaiian strain and lowest for the Mekong strain for all growth traits. Reciprocal effects influenced negatively on growth rate of crosses with the Hawaiian (H) strain as dams and the Dong Nai (D) or Mekong (M) as sires compared with their reciprocal crosses (DH and MH). Heterotic effects for all growth traits were small and not significantly different from zero (P > 0.05). These results indicate that a crossbreeding approach based on the strains evaluated here provides only limited potential for improving growth rates based simply on heterotic outcomes and that a likely more productive option would be to trial artificial selection on a diverse synthetic stock. The current study also employed genetic markers (microsatellites) to characterize levels and patterns of genetic diversity in three purebred strains of GFP that originated from the diallel cross above. All three purebred strains showed relative high levels of genetic diversity in terms of allele number and individual heterozygosity across the six marker loci screened. Levels of genetic diversity present in the three purebred strains combined into a single stock were compared with that from a combination of three wild river stocks to assess the impact of domestication on genetic diversity of a ‘synthetic’ population. Results demonstrated that there was no significant loss of genetic diversity in the three purebred strains combined compared with a reference set containing the three wild populations. Therefore, a synthetic population formed from these purebred strains successfully captured the majority of genetic variation present in the wild broodstock. This synthetic population provides a potential stock for a future selective breeding program for GFP in Vietnam. The current study was also the first attempt to identify single nucleotide polymorphisms (SNPs) in key growth genes in GFP. Two key candidate genes were targeted, actin and crustacean hyperglycemic hormone (CHH), that are potentially linked to growth performance in GFP. The study screened SNPs in GFP females only, because growth performance of GFP males is influenced strongly by social rank. The study identified four SNPs in intron 3 of the CHH gene that were significantly correlated with individual body weight at harvest, while no SNPs detected in the actin gene were associated with growth traits in GFP. This finding however, needs to be confirmed using larger sample sizes and other GFP lines. The current study has produced important basic knowledge relevant to implementation of an effective stock improvement program for GFP in Vietnam. Results indicate that a selective breeding strategy rather than a crossbreeding approach is likely to be the best strategy for improving GFP culture stocks in Vietnam. In addition, the study demonstrates that application of modern molecular genetic technologies can be efficient in developing a genetically diverse, synthetic population for stock improvement and for identifying potential markers correlated with important commercial traits in GFP. Integration of DNA techniques with traditional breeding practices can facilitate GFP stock improvement in Vietnam and accelerate the industry development when improved lines are available. Some limitations of the current study and recommendations for further work are discussed.

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. / The European sea bass (Dicentrarchus labrax) is a major species of Mediterranean aquaculture, the production of which rose from almost nothing in 1985 to more than 100.000 tonnes annually at present. In many cases, wild-caught broodstock is still used to produce juveniles for aquaculture, and farmed population are predominantly male – which unfortunately perform less than females. The aim of the present research was first to quantify the genetic variation of growth and sex ratio between families of sea bass produced by artificial fertilization and reared in a “common garden” approach, using the genotyping of microsatellite markers to reconstruct the pedigrees. In a second phase, we also studied the response in terms of growth and sex ratio to an experimental selection applied on body length.We first could show that the experimental technique chosen (artificial fertilization, common garden rearing and pedigree reconstruction by genotyping) was efficient and could be applicable not only to conduct experiments but also to set up breeding programmes in sea bass.Growth is a heritable trait in sea bass, with a high heritability for body weight at commercial size (h²=0.38-0.44 around 400 g mean weight), but a lower value for growth rate from 35 to 400g (0.16-0.34), showing the importance of the highly heritable (h²=0.61) early growth in the building of the performance at commercial size. Additionally, we showed that sea bass growth was not significantly impacted by dominance or non genetic maternal effects. We estimated genotype by environment interactions for growth between highly divergent ongrowing sites, showing that although interactions were moderate for body weight at commercial size (rA= 0.70-0.99 between sites), they were much higher for growth rate (rA=0.21-0.61 between sites). Although we purposely chose very divergent ongrowing environments, this highlights the importance of conducting breeding programs in environments resembling the production environment.We showed that the sex ratio of natural populations in the wild did not differ from 50-50 on average, although some age classes could have a biased sex ratio, probably due to environmental effects. In a farmed population, sex ratios were shown to differ between families and to be equally influenced by the sire and the dam. No purely genetic model could account for the distributions observed, which could fit either to a model with a minimum of two bi-allelic loci plus micro-environmental variance, or to a polygenic threshold model with h²=0.62 for sex tendency on the underlying scale. This last model also revealed a positive genetic correlation (rA=0.50) between sex tendency and growth. This allowed us to predict that domestication should tend towards a balancing of the sex ratio at 50-50, while selection for faster growth should bias population sex ratios towards females. This is precisely what we observed later on in our selection response experiment, which also confirmed the potential of the species to be selected for faster growth, with a 23% gain in body weight in the first generation.The polygenic (or at least polyfactorial) model of sex determination is considered rare in Vertebrates. After developing its possible use to tend towards monosex female farmed populations of sea bass, we assessed its position in the theory of sex determination in ectotherm Vertebrates, where it seems that it could well be more frequent as initially thought. Polygenic sex determination could be a means for species and populations to move along the ESD-GSD continuum (Environmental or Genetic Sex Determination).

Jatropha curcas L., também conhecida no Brasil como pinhão-manso, é uma oleaginosa que atraiu a atenção do mundo para bioenergia dado a qualidade e o alto conteúdo de óleo na semente. Contudo, a espécie necessita de programas de melhoramento genético para fixar características de interesse em bancos de germoplasma. Este trabalho objetivou identificar e analisar a diversidade alélica, metabólica e físico-química relacionada à síntese de óleo e ésteres de forbol em uma amostra de 22 genótipos do BAG do Instituto Agronômico de Campinas para seleção de genótipos elite. Os genes MFP2, KASIII e 3-N-D, envolvidos na biossíntese de óleo e de taxol, foram selecionados a partir de Gomes et al. (2010). Os resultados mostraram que há baixa diversidade alélica para os genes KAS III e MFP2, por outro lado, a expressão desses mesmos genes e a composição de ácidos graxos foi bastante variável entre os genótipos e ao longo do desenvolvimento da semente de J. curcas indicando uma provável regulação diferenciada da via de óleo. O estudo realizado permite combinar a diversidade alélica, expressão dos genes, conteúdo metabólico e poder calorífico para a seleção de genótipos e identificação de parentais direcionando cruzamentos no quadro do programa de melhoramento do IAC. / Jatropha curcas L., also know in Brazil as physic nut, is an oilseed that call world´s attention to bioenergy due to quality and high oilseed content. However, this species needs of breeding programs so that interest traits may to be fixed in germplasm banks. This study aimed to identify and analyze allelic, metabolic and physicochemical diversity related to oil and phorbol esters synthesis in a 22 genotypes sample from Instituto Agronômico de Campinas-BAG for elite genotypes selection. The MFP2, KASIII and 3-ND genes involved in oil and taxol biosynthesis were selected from Gomes et al. (2010). The results showed that there is low allelic diversity for KAS III and MFP2 genes, on the other hand, the expression of these same genes and fatty acid composition was quite variable between genotypes through J. curcas seed development indicating a putative differential regulation in oil pathway. This study allows combining allelic diversity, gene expression, metabolic content and calorific values for parental genotypes identification and selection driving crosses within IAC breeding program.

Indiana University-Purdue University Indianapolis (IUPUI) / Stress has been shown to contribute to alcohol drinking; however, inconsistencies in both the clinical and pre-clinical literature speak to the need for better paradigms to study this interaction. The present experiments compared animal models of the propensity to consume ethanol, the selectively bred alcohol-preferring (P) and high-alcohol-drinking (HAD) rat lines, in their response to yohimbine on ethanol seeking and self-administration and anxiety-like behavior. The P and HAD lines consume similar amounts of ethanol, yet differ in apparent motivation to drink ethanol, in anxiety-like behavior, and response to stress in alcohol drinking. Therefore, it was of interest to determine whether stress may differentially affect ethanol-motivated behaviors between the P and HAD lines. Acute administration of yohimbine, an α-2 adrenoreceptor antagonist that increases anxiety and activate stress systems, increased operant ethanol self-administration and reinstatement of ethanol seeking in P rats, and free-choice ethanol drinking in both P and HAD rats. However, acute yohimbine administration decreased ethanol drinking when given limited access in the home cage, an effect that was diminished by extending the pre-treatment interval or increasing the number of ethanol exposure sessions. Yohimbine did not alter appetitive responding during a non-reinforced trial, nor did yohimbine alter the acquisition of free-choice ethanol drinking. Exposure to alcohol deprivation resulted in modest increases in ethanol intake, but yohimbine did not potentiate this effect. While acute yohimbine administration increased anxiety-like behavior, prior experience with repeated yohimbine exposures or with repeated deprivation periods did not. P rats were shown to be more active and less anxious and to display greater responding during a non-reinforced trial than HAD rats. Taken together, the results of these experiments demonstrate that the timing of yohimbine exposure relative to ethanol access is a critical component to determining its effects on ethanol seeking and self-administration and anxiety-like behavior. Further investigation into the parameters under which stress alters the motivation to seek and consume ethanol between these selectively bred lines is warranted, and future work that incorporates therapeutic agents aimed at reducing stress reactivity and alcohol drinking could elucidate effective strategies in the treatment of alcoholism.

Les parasitoïdes se développent sur, ou, à l'intérieur d'un hôte qu’ils tuent au cours de leur développement. Ils sont souvent utilisés en lutte biologique car ils ont la capacité de réduire et de contrôler les populations d’organismes considérés comme nuisibles. Nous avons investigué la capacité de la guêpe parasitoïde Telenomus podisi à induire l’avortement des oeufs de son hôte : la punaise exotique Halyomorpha halys. Cette nouvelle association d’espèce ne permet pas à la guêpe de se reproduire, mais elle induit un taux d’avortement des oeufs de l’hôte, néanmoins variable d’une guêpe à l’autre. Nos trois expériences ont permis de déterminer que 1) le taux d’avortement suit la grosseur de l’oeuf, qu’il soit parasité ou non. Que ce taux d’avortement est encore plus important lorsque parasité par des guêpes de plus petite taille. 2) Le taux d'avortement est expliqué à 18.2% par la génétique des guêpes (h2 = 0,182). 3) Il est difficile de générer une population de T. podisi capable d’induire un taux d’avortement élevé après 5 générations de reproduction sélective. Nous ouvrons, par ces résultats, une piste en matière de lutte biologique contre l’insecte ravageur qu’est H. halys. L’utilisation de petites guêpes permettrait de réduire la reproduction de la punaise. Mais aussi, qu’à la lumière du contenu de ce mémoire, un programme de reproduction sélective pourrait être optimisé pour produire des guêpes performantes en matière d’avortement des oeufs de H. halys. / Parasitoids develop on, or, inside a host they kill during their development. They are often used in biological control because they have the ability to reduce and control populations of organisms considered harmful. We investigated the ability of the parasitoid wasp Telenomus podisi to induce the abortion of its host eggs: the exotic stink bug Halyomorpha halys. This new species association does not allow the wasp to reproduce, but it induces some abortion of the eggs of the host, nevertheless variable from one wasp to another. Our three experiments have determined that 1) the abortion rate follows the size of the egg, whether parasitized or not. That this abortion rate is even greater when parasitized by smaller wasps 2) The abortion rate is explained to 18.2% by wasp genetics (h2 = 0.182). 3) It is difficult to generate a population of T. podisi capable of inducing a high abortion rate after 5 generations of selective breeding. With these results, we are opening a track in biological control against the pest insect H. halys. The use of small wasps would reduce the stink bug reproduction. But also, at the light of the contents of this thesis, a selective breeding program could be optimized to produce efficient wasps in the abortion of H. halys eggs.

Indiana University-Purdue University Indianapolis (IUPUI) / Multiple lines of High Alcohol Preferring (HAP) mice were selectively bred for their intake of 10% ethanol (v/v) during 24-h daily access over a four-week period, with the highest drinking lines exhibiting intakes in excess of 20 g/kg/day. Drinking rhythms and corresponding blood ethanol concentrations (BEC) of the highest drinking HAP lines to those of the C57BL/6J (B6) inbred strain. Adult male and female crossed HAP (cHAP), HAP1 and B6 mice had free-choice access to 10% ethanol and water for 3 weeks prior to bi-hourly assessments of intake throughout the dark portion of a reverse 12:12 light dark cycle. In another cohort of cHAP mice, the same procedure was used to assess bi-hourly ethanol intake, and blood samples were taken across the day to look at the pattern of accumulation in these mice. Finally, considering the high level of intake by cHAP mice, we were interested in assessing whether metabolic and functional tolerance develop following chronic free-choice access, which were assessed using 2.0 and 1.75 g/kg challenge doses of 20% ethanol, respectively. cHAP and HAP1 mice maintained an excessive level of intake throughout the dark portion of the cycle, accumulating mean BEC levels of 261.5 + 18.09 and 217.9 + 25.02 mg/dl at 7-8 hours following lights off, respectively. B6 mice drank comparatively modestly, and did not accumulate high BEC levels (53.63 + 8.15 mg/dl). In the cHAP cohort, mean BECs were 112.47 + 19.91 at 2 hours after lights off, 189.00 + 27.40 at 6 hours after lights off, 193.80 + 29.66 at 10 hours after lights off, and 89.68 + 22.19 at 2 hours after lights on. Further, following 3 weeks of ethanol access, cHAP mice had a faster rate of ethanol metabolism and fewer hind slips than water-only exposed mice (ps < .05). In conclusion, the excessive free-choice drinking demonstrated by the HAP1 and cHAP lines, as well as the pattern of sustained high BECs in cHAP mice, challenge the notion that rodents will not reliably and voluntarily sustain ethanol intake at pharmacologically relevant levels. These results suggest that the highest drinking HAP lines may provide a unique opportunity for modeling the excessive intake that has been observed in alcohol-dependent individuals. Further, we observed that cHAP mice develop both metabolic and functional tolerance to the ataxic effects of ethanol following 3 weeks of free-choice access. Together, these findings support HAP mice as translational rodent model of alcoholism, and provide rationale for exploration of the predisposing factors for excessive consumption, as well as the development of physiological, behavioral, and toxicological outcomes following alcohol exposure.

Tesis por compendio / [ES] La acuicultura se proyecta como un medio vital para alimentar de manera sostenible a la creciente población mundial. Sin embargo, para lograrlo, la producción de peces debe abordarse con sostenibilidad y adaptabilidad en mente, especialmente frente a desafíos como el cambio climático y la disminución de recursos. Esto requiere innovaciones en genética y nutrición para garantizar la resiliencia de las poblaciones de peces cultivados. Comprender las interacciones entre organismos, microbiota y el medio ambiente es crucial, y las tecnologías ómicas ofrecen una manera de profundizar en estas dinámicas. Se ha secuenciado el genoma del dorado, una especie significativa de acuicultura europea, lo que ha llevado a conocer la expansión génica y la plasticidad fenotípica. Esta tesis tuvo como objetivo aprovechar este conocimiento integrando diversas aproximaciones ómicas para anotar el genoma y la microbiota intestinal de esta importante especie mediterránea. El enfoque se centró en acciones para hacer más sostenibles las prácticas futuras de acuicultura. Un aspecto crítico abordado fue la gestión de los niveles de oxígeno, dada su disminución debido al cambio climático. Comprender las respuestas de los peces al oxígeno reducido es vital para la acuicultura sostenible. La investigación sobre el dorado reveló adaptaciones a la hipoxia leve, incluida una disminución general de la respuesta metabólica y variaciones a nivel de expresión génica. La selección genética y los avances en piensos acuícolas también son esenciales para la acuicultura sostenible. La tesis monitoreó la evolución de los peces y la dieta junto con un programa de cría para el crecimiento, revelando respuestas diferenciales en peces alimentados con recursos marinos reducidos. La selección genética por un crecimiento rápido es capaz de influir en la composición y la actividad de la microbiota intestinal. La caracterización de esta comunidad también reveló su importancia en la salud y el crecimiento de los peces. Los factores genéticos parecían jugar un papel más importante que la dieta en la formación de la composición de la microbiota intestinal, pero las interacciones entre genética y dieta influenciaron tanto las respuestas del huésped como las microbianas. En resumen, la tesis presenta resultados prometedores para mejorar el crecimiento, la salud y la adaptación ambiental en especies de acuicultura, contribuyendo también a la sostenibilidad del sector acuícola. / [CA] L'aqüicultura es projecta com un mitjà vital per a alimentar de manera sostenible la creixent població mundial. No obstant això, per a aconseguir-ho, la producció de peixos ha d'abordar-se amb sostenibilitat i adaptabilitat en ment, especialment front a desafiaments com el canvi climàtic i la disminució de recursos. Això requereix innovacions en genètica i nutrició per a garantir la resiliència de les poblacions de peixos cultivats. Comprendre les interaccions entre organismes, microbiota i el medi ambient és crucial, i les tecnologies òmiques oferixen una manera de profunditzar en aquestes dinàmiques. S'ha sequenciat el genoma de l'orada, una espècie significativa d'aqüicultura europea, la qual cosa ha portat a conèixer l'expansió gènica i la plasticitat fenotípica de l'espècie. Aquesta tesi té com a objectiu aprofitar aquest coneixement integrant diverses aproximacions òmiques per a anotar el genoma i la microbiota intestinal d'aquesta important espècie mediterrània. L'enfocament es va centrar en accions per a fer més sostenibles les pràctiques futures d'aqüicultura. Un aspecte crític abordat va ser la gestió dels nivells d'oxigen, donada la seua disminució a causa del canvi climàtic. Comprendre les respostes dels peixos a l'oxigen reduït és vital per a l'aqüicultura sostenible. La investigació va revelar adaptacions a la hipòxia lleu, inclosa una disminució general de la resposta metabòlica i variacions a nivell d'expressió gènica. La selecció genètica i els avanços en pinso per a l'aqüicultura també són essencials per a la sostenibilitat del sector. La tesi va monitorar l'evolució dels peixos i la dieta juntament amb un programa de sel·lecció genètica per creixement, revelant respostes diferencials en peixos alimentats amb recursos marins reduïts. La selecció genètica per a un creixement ràpid és capaç d'influir en la composició i l'activitat de la microbiota intestinal. La caracterització d'aquesta comunitat també va revelar la seua importància en la salut i el creixement dels peixos. Els factors genètics semblaven jugar un paper més important que la dieta en la formació de la composició de la microbiota intestinal, però les interaccions entre genètica i dieta van influir tant en les respostes de l'organisme com en les microbianes. En resum, la tesi presenta resultats prometedors per a millorar el creixement, la salut i l'adaptació ambiental en espècies d'aqüicultura, contribuint també a la sostenibilitat del sector aqüícola. / [EN] Aquaculture is projected as a vital means to feed the growing global population sustainably. However, to achieve this, fish production must be approached with sustainability and adaptability in mind, especially in the face of challenges like climate change and resource depletion. This requires innovations in genetics and nutrition to ensure the resilience of farmed fish populations. Understanding the interactions between organisms, microbiota, and the environment is crucial, and omics technologies offer a way to delve deeper into these dynamics. The genome of the gilthead sea bream, a significant European aquaculture species, has been sequenced, leading to insights into gene expansion and phenotypic plasticity. This thesis aimed to leverage this knowledge by integrating various omics approaches to annotate the genome and gut microbiome of this important Mediterranean species. The focus was on actions to conserve and "green" future aquaculture practices. One critical aspect addressed was the management of oxygen levels, given their declining availability due to climate change. Understanding fish responses to reduced oxygen is vital for sustainable aquaculture. Research on gilthead sea bream revealed adaptations to mild hypoxia, including a hypo-metabolic general response and changes in metabolic processes and gene expression profiling. Selective breeding and advancements in aquafeeds are also essential for sustainable aquaculture. The thesis monitored fish and diet evolution alongside a breeding program for growth, revealing differential responses in fish fed with reduced marine resources. Genetic selection for fast growth influenced the gut microbiota, highlighting the interconnectedness of genetics, diet, and microbial communities. Characterization of the gut microbiota revealed its importance in fish health and growth. Genetic factors appeared to play a more significant role than diet in shaping the gut microbiota composition, but interactions between genetics and diet influenced both host and microbial responses. Overall, the thesis presents promising outcomes for enhancing growth, health, and environmental adaptation in aquaculture species. By understanding the interconnectedness of genetics, nutrition, and microbiota, it aims to contribute to the sustainability of the aquaculture sector. / This PhD thesis has been elaborated by the PhD candidate thanks to two research contracts appointed to the framework of two H2020 European projects: AQUAEXCEL2020 “AQUAculture infrastructures for EXCELlence in European fish research towards 2020” (2015-2020; grant agreement nº 652831), and AquaIMPACT “Genomic and nutritional innovations for genetically superior farmed fish to improve efficiency in European aquaculture” (2019-2023; grant agreement nº 818367). During the thesis, the candidate completed a 3-months (91 days) stay in the Centre for Integrative Genetics (CIGENE), belonging to the Norwegian University of Life Sciences (NMBU) in Ås, Norway. This stay was financed by an EMBO Scientific Exchange Grant (grant agreement nº 10168). A grant from the iMOVE program from CSIC (grant agreement nº IMOVE23080) was also awarded, but not financially executed. Core publications of this thesis were funded by: AQUAEXCEL2020 H2020 EU Project (652831); PerformFISH H2020 EU Project (H2020-SFS-2016-2017; 727610); AquaIMPACT H2020 EU Project (818367); ThinkInAzul (THINKINAZUL/2021/024, PRTR-C17.I1); Bream-AquaINTECH (RTI2018–094128-B-I00); The rest of publications in which the candidate was involved received extra funding from: GAIN H2020 EU Project (773330) y AQUAEXCEL3.0 H2020 EU Project (871108) / Naya Català, F. (2024). The Two Genomes of Gilthead Sea Bream (Sparus aurata): a Multi-Omics and Holobiont Approach [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/205692 / Compendio