The aim of the work was to evaluate the effect of different protein and lipid sources of animal and vegetable origin on the reproductive performance of black catfish Rhamdia quelen females. Three experiments were accomplished with duration of 90 days each, divided in three phases: Phase I, Reproducers feeding; phase II, Induced reproduction and eggs and larvae incubation; phase III, Larvae culture. Fifteen females of black catfish (around 700g) were used for experiments 1 and 2, and 500g for experiment 3. The females were distributed in three net cages of 1m³, 5 fish (4 females for induction and 1 for oocyte collection). The fish were fed for ten weeks using three diets as treatments: experiment 1, meat and bone meal and soybean meal (CS), fish meal and soybean meal (PS) and yeast and soybean meal (LS); For experiment 2, the effect of substitution of the meat and bone meal for the soybean meal in increasing levels was evaluated (0%, 35%, 70%), that were treatments CS 0, CS 35 and CS 70; In experiment 3, pork fat (BP), sunflower oil (OG) and Canola oil (OC). After induced spawning, samples of ten eggs were collected at the moment of the fishes spawning, at 3, 9, 12, 18 and 24 hours. Also samples of ten larvae were collected, at the moment of the eclosion, at 12, 24, 36 and 48 hours. Three samples of larvae of each incubator in the density of 30 larvae/l, were collected and fed during 14 days. Changeable zoogenic were esteem for phases I and III and reproductive for phase II. In experiment 1, females fed with the diet of treatment LS, had shown minor profit in weight, the eggs had equally minor weight. For the embryonic evelopment treatments, CS and PS were superior to treatment LS in the variable (DSV). In the larval development in the incubators, treatment CS showed better performance for the variable (CT). For the experiment 2, females fed with diets CS 70, had not answered the spawning of fishes. The embryonic development, larval vitelline and larvae were superior in treatment CS 0 for the variable (DO and AO), (CT and AT), (CT, CP, Area, SOB) respectively. In experiment 3, the larvae development in the incubators, treatment BP was minor that treatment OG in the variable (CT), equally treatment BP was minor that treatments OG and OC for the variable (DSV). For the larval development until the 14 days treatment OC was greater that treatment BP for the variable (CT and CP). We can conclude that the use of Meat and Bone meal and Soybean meal as protein sources are presented as good option in the feeding of reproductive females of black catfish. The pork fat is so good as sunflower and canola oils as lipid sources for reproductive females and they provide good development of the embryo and jundiá s larvae / No trabalho avaliou-se o efeito de diferentes fontes protéicas e lipídicas de origem animal e vegetal sobre o desempenho reprodutivo de fêmeas de jundiá Rhamdia quelen. Foram realizados três experimentos, de 90 dias cada, divididos em três fases: fase I, Alimentação de reprodutores; fase II, Reprodução induzida e incubação de ovos e larvas; fase III, Larvicultura. Foram utilizadas 15 fêmeas de jundiá com peso aproximado de 700g para os experimentos 1 e 2, e 500g para o experimento 3. As fêmeas foram distribuídas em três tanques-rede de 1m³, sendo 5 peixes por tanque rede (4 fêmeas para indução e 1 para coleta de ovócitos) e alimentadas durante dez semanas com três dietas experimentais. No experimento 1 testaram-se Farinha de Carne e Ossos e Farelo de Soja (CS), Farinha de Peixe e Farelo de Soja (PS) e Levedura de Cana e Farelo de Soja (LS). No experimento 2, avaliou-se o efeito de substituição da Farinha de Carne e Ossos pelo Farelo de Soja na ração CS do experimento 1 em níveis crescentes, sendo os tratamentos CS 0, CS 35 e CS 70. No experimento 3, testaram-se a Banha de Porco (BP), Óleo de Girassol (OG) e Óleo de Canola (OC) como fontes de lipídios. Após desova, foram coletadas amostras de dez ovos, às 0, 3, 9, 12, 18 e 24 horas. Após a eclosão foram coletadas amostras de dez larvas às 0, 12, 24, 36 e 48 horas e medidas, e três amostras de larvas de cada incubadora foram alimentadas durante 14 dias. Foram estimadas variáveis zootécnicas para as fases I e III e reprodutivas para fase II. No experimento 1, as fêmeas do tratamento LS, mostraram menor ganho em peso, igualmente os ovos tiveram menor peso. Para o desenvolvimento embrionário os tratamentos CS e PS foram superiores ao tratamento LS na variável Diâmetro do Saco Vitelino (DSV). No desenvolvimento larval nas incubadoras, o tratamento CS mostrou melhor desempenho para Comprimento Total (CT). No experimento 2, as fêmeas alimentadas com dieta CS 70, não responderam a desova. O desenvolvimento embrionário, larval vitelino e larval foi superior no tratamento CS 0 para as variáveis (DO e AO), (CT e AT), (CT, CP, Área, SOB), respectivamente. No experimento 3, no desenvolvimento das larvas nas incubadoras, o tratamento BP foi menor que o tratamento OG na variável (CT), e igualmente o tratamento BP foi menor que os tratamentos OG e OC para a variável (DSV). Para o desenvolvimento larval até os 14 dias o tratamento OC foi maior que o tratamento BP para as variáveis (CT e CP). Conclui-se que a farinha de carne e ossos e farelo de soja (até 60% de inclusão) são boas fontes protéicas para fêmeas reprodutoras de jundiá. A banha de porco é tão eficiente quanto óleo de girassol e canola como fontes lipídicas para fêmeas reprodutoras e proporcionam bom desenvolvimento embrionário e das larvas de jundiá

Au cours des dernières années, l'augmentation de la production aquacole a nécessité un changement dans la composition des aliments pour poissons, pour remplacer la farine (FP) et l’huile de poisson (HP) par des sources végétales plus disponibles. Dans ce contexte, le travail de ma thèse avait pour but d'analyser les effets d’une substitution totale et concomitante de la FP et HP par des ingrédients végétaux dans les aliments distribués pendant tout le cycle de vie de la truite arc-en-ciel, de la première alimentation jusqu’à la reproduction. Ce travail a montré pour la première fois que la truite peut survivre, se développer et avoir une descendance viable, lorsqu’elle est nourrie tout au long de son cycle de vie avec un régime 100% végétal. Un tel remplacement alimentaire a entraîné des changements radicaux dans le profil en acides gras des tissus des femelles. Cependant, nous avons constaté que la truite était capable de synthétiser des acides gras polyinsaturés à longue chaîne n-3 (AGPI-LC n-3) à partir de précurseurs présents dans l'aliment, et de stocker dans les ovules une partie de ces acides gras néosynthétisés dans le foie , permettant ainsi une reproduction efficace. Nous avons également étudié les possibles effets trans-générationnels d’une alimentation 100% végétale des géniteurs, sur la survie et la croissance de la descendance et sur sa réponse à différents régimes aux stades précoces, en nous appuyant sur des analyses du transcriptome des alevins entiers. Aucun effet significatif de l’alimentation maternelle avec des régimes à base de végétaux n’a été observé sur les descendants avant leur première alimentation, à l'exception d'un poids corporel légèrement inférieur (-13%) à celui des descendants de femelles nourries avec un aliment contenant des FP et HP. En revanche, des effets significatifs de l'alimentation maternelle sur le transcriptome des alevins sont apparus après 3 semaines d'alimentation. L'histoire nutritionnelle de la mère a affecté principalement des gènes impliqués dans la croissance/contraction musculaire et dans les métabolismes énergétique et glucidique. Quelle que soit l'origine maternelle, l’alimentation des alevins avec des aliments contenant des ingrédients végétaux conduit à une régulation positive des gènes impliqués dans le métabolisme des AA/protéines et le métabolisme du cholestérol, ainsi qu’à des changements dans l'expression des gènes impliqués dans le métabolisme glucidique. Enfin, les effets à long-terme de régimes à base de matières premières végétales chez la truite arc-en-ciel ont également été étudiés chez les juvéniles (10g) et les poissons «en croissance» (250-350g), en se focalisant principalement sur l’expression des gènes dans l’intestin et le foie. Cette étude à long-terme a mis en évidence chez les juvéniles des effets subtils sur des gènes intestinaux et hépatiques (transcriptome), avec principalement une augmentation de l’expression des gènes impliqués dans les voies de synthèse des AGPI-LC et du cholestérol chez les poissons nourris avec des régimes à base de plantes. Ces changements d’expression ont été maintenus chez les poissons «en croissance». L'expression de gènes impliqués dans le catabolisme des protéines, le métabolisme des glucides et dans le transport intracellulaire a également été modifiée par les régimes à base de plantes chez les juvéniles, mais ces résultats ne sont pas entièrement confirmés chez les poissons «en croissance». L'ensemble des résultats de cette thèse fournissent des informations originales sur l'utilisation de régimes alimentaires avec des taux de remplacement élevés de FP et d’HP pendant l'ensemble du cycle de vie des poissons, y compris les reproducteurs et les stades précoces, car la majorité des études précédentes avaient concerné la phase de grossissement. Des ajustements de la formule alimentaire sont encore nécessaires pour continuer à optimiser les performances de reproduction et la croissance des poissons d’élevage. / In the last years, the increase in aquaculture production has forced a change in fish feed composition, with increasing substitution of fish meal and fish oil by more available plant sources. In this context, the present PhD work aimed at analyzing the effects of different levels of concomitant dietary replacement of fish meal and fish oil by plant ingredients during the whole life cycle of rainbow trout (from first feeding to reproduction). This work showed for the first time that rainbow trout was able to survive, grow and produce viable offsprings, when fed a totally plant-based diet throughout the whole life cycle. Such dietary replacement resulted in drastic changes in tissues fatty acid profile of broodstock females. However, we found that trout was capable to synthetize n-3 long chain- polyunsaturated fatty acids (LC-PUFA) from dietary precursors and to transfer large amounts of these fatty acids in ova, so that an efficient reproduction can occur. We also studied the potential carry over generation effects of feeding broodstock a totally plant-based diet on progeny and their response to different diets at early stages, using molecular approaches, including the study of the whole body transcriptome. Considering the effects on progeny, the present study confirmed the capability of trout to survive and grow on a plant-based diet, but with slight differences in terms of weight. While no effects of maternal dietary background were observed before first feeding, except slightly lower body weight (-13%), significant effects on the transcriptome of whole body alevins appeared after 3 weeks of feeding. These effects of maternal nutritional history were mainly related to muscle growth/contraction and carbohydrate and energy metabolism. Irrespective of the maternal origin of progeny, first feeding diets containing plant ingredients resulted in up-regulation of genes involved in AA/protein and cholesterol metabolism, as well as in changes in the expression of genes involved in carbohydrate metabolism. Finally, the effects of long-term feeding trout plant-based diets were also studied in juveniles (10g) and ongrowing fish (250-350g), mainly focusing on intestine and liver gene expression. The long term trial in juveniles highlighted subtle effects on both intestinal and hepatic gene expression (transcriptome), mainly related to LC-PUFA and cholesterol biosynthetic pathways, which were enhanced in fish fed the plant based diets. This transcriptional pattern was maintained in ongrowing fish. Genes involved in protein catabolism, carbohydrate metabolism and trafficking were also affected by plant-based diets in juveniles, but these results were not fully confirmed in ongrowing fish. Overall, the results of the present thesis allowed extending the use of diets with high replacement rates of fish meal and fish oil to the whole life cycle of fish, including broodstock and early stages. Adjustments of the feed-formula are still needed to further optimize reproductive and growth performance.

The United States Pacific Northwest is well known for its shellfish farming. Historically, commercial harvests were dominated by the native Olympia oyster, Ostrea lurida, but over-exploitation, habitat degradation, and competition and predation by non-native species has drastically depleted their densities and extirpated many local populations. As a result, shellfish aquaculture production has shifted to the introduced Pacific oyster, Crassostrea gigas. An underlying objective of this dissertation is the use of molecular genetics to improve our ability to accurately identifying optimal oyster broodstock for either restoration of Olympia oysters or farming of Pacific oysters. The ecological benefits provided by oysters as well as the Olympia oyster's historical significance, has motivated numerous restoration/supplementation efforts but these efforts are proceeding without a clear understanding of the genetic structure among extant populations, which could be substantial as a consequence of limited dispersal, local adaptation and/or anthropogenic impacts. To facilitate this understanding, we isolated and characterized 19 polymorphic microsatellites and used 8 of these to study the genetic structure of 2,712 individuals collected from 25 remnant Olympia oyster populations between the northern tip of Vancouver Island BC and Elkhorn Slough CA. Gene flow among geographically separated extant Olympia oyster populations is surprisingly limited for a marine invertebrate species whose free-swimming larvae are capable of planktonic dispersal as long as favorable water conditions exist. We found a significant correlation between geographic and genetic distances supporting the premise that coastal populations are isolated by distance. Genetic structure among remnant populations was not limited to broad geographic regions but was also present at sub-regional scales in both Puget Sound WA and San Francisco Bay CA. Until it can be determined whether genetically differentiated O. lurida populations are locally adapted, restoration projects and resource managers should be cautious of random mixing or transplantation of stocks where gene flow is restricted. As we transition from our Olympia oyster population analysis to our Pacific oyster quantitative analysis, we recognize that traditional quantitative trait locus (QTL) mapping strategies use crosses among inbred lines to create segregating populations. Unfortunately, even low levels of inbreeding in the Pacific oyster (Crassostrea gigas) can substantially depress economically important quantitative traits such as yield and survival, potentially complicating subsequent QTL analyses. To circumvent this problem, we constructed an integrated linkage map for Pacific oysters, consisting of 65 microsatellite (18 of which were previously unmapped) and 212 AFLP markers using a full-sib cross between phenotypically differentiated outbred families. We identified 10 linkage groups (LG1-LG10) spanning 710.48 cM, with an average genomic coverage of 91.39% and an average distance between markers of 2.62 cM. Average marker saturation was 27.7 per linkage group, ranging between 19 (LG9) and 36 markers (LG3). Using this map we identified 12 quantitative trait loci (QTLs) and 5 potential QTLs in the F1 outcross population of 236 full-sib Pacific oysters for four growth-related morphometric measures, including individual wet live weight, shell length, shell width and shell depth measured at four post-fertilization time points: plant-out (average age of 140 days), first year interim (average age of 358 days), second year interim (average age of 644 days) and harvest (average age of 950 days). Mapped QTLs and potential QTLs accounted for an average of 11.2% of the total phenotypic variation and ranged between 2.1 and 33.1%. Although QTL or potential QTL were mapped to all Pacific oyster linkage groups with the exception of LG2, LG8 and LG9, three groups (LG4, LG10 and LG5) were associated with three or more QTL or potential QTL. We conclude that alleles accounting for a significant proportion of the total phenotypic variation for morphometric measures that influence harvest yield remain segregating within the broodstock of West Coast Pacific oyster selective breeding programs. / Graduation date: 2012