Impact of genotypic errors with equal and unequal family contribution on accuracy of genomic prediction in aquaculture using simulation.

Genotypic errors, conflict between recorded genotype and the true genotype, can lead to false or biased population genetic parameters. Here, the effect of genotypic errors on accuracy of genomic predictions and genomic relationship matrix are investigated using a simulation study based on population and genomic structure comparable to black tiger prawn, Penaeus monodon. Fifty full-sib families across five generations with phenotypic and genotypic information on 53 K SNPs were simulated. Ten replicates of different scenarios with three heritability estimates, equal and unequal family contributions were generated. Within each scenario, four SNP densities and three genotypic error rates in each SNP density were implemented. Results showed that family contribution did not have a substantial impact on accuracy of predictions across different datasets. In the absence of genotypic errors, 3 K SNP density was found to be efficient in estimating the accuracy, whilst increasing the SNP density from 3 to 20 K resulted in a marginal increase in accuracy of genomic predictions using the current population and genomic parameters. In addition, results showed that the presence of even 10% errors in a 10 and 20 K SNP panel might not have a severe impact on accuracy of predictions. However, below 10 K marker density, even a 5% error can result in lower accuracy of predictions.

Evaluation of Dunaliella salina growth and corresponding ß-carotene production in tubular photobioreactor / Avaliação do crescimento da Dunaliella salina e correspondente produção de ß-caroteno em fotobiorreator tubula

Microalgae, photosynthetic microorganisms, are rich in lipids, polyunsaturated fatty acids, carbohydrates, proteins, vitamins, as well as carotenoids, which are antioxidants that may protect human body from various diseases including obesity, cardiovascular disease, vision-related diseases such as macular degeneration and certain types of cancer. These natural pigments have applications in the pharmaceutical (nutraceutical), food (coloring, functional food, and supplements), and cosmetics industries (e.g. sunscreen), as well as in aquaculture (animal feed). The Dunaliella salina microalga can synthesize 10% of dry weight in ß-carotene (orange pigment, pro-vitamin A activity) under high light intensity and nitrogen and phosphorus limitation, among other stress conditions. The first chapter of this thesis presents a review focused on microalgae carotenoids: culture systems, mode of operation, and applications. In this bibliographic survey, the advantages of microalgae cultivation in relation to traditional sources (higher plants) were discussed, as well as a discussion of the main cultivation systems and their importance in cell growth. This review presented a critical analysis of the different operational regimes like batch, fed-batch, semi-continuous and continuous. Relevant information on the most important world producers of microalgae carotenoids were presented. Chapter II presents the development of a modified method of dispersive liquid-liquid microextraction (DLLME) for rapid extraction of ß-carotene from Dunaliella salina cultivated in tubular photobioreactor, with subsequent development of a rapid chromatographic screening method using a C4 column for separation of geometric isomer of ß-carotene. The use of benzene as extraction solvent and water with 50% acetone as dispersant provided the best condition for the extraction of this carotenoid. In HPLC (High Performance Liquid Chromatography), employing mobile phase composed of methanol and water (95:5, v/v), it was possible to detect/quantify ß-carotene at 14 min (retention time). Besides the short analysis time (<20 min), by the miniaturized extraction (< 10 mL organic waste) this method abide by green chemistry analytical principles. It is known that nitrogen, phosphorus, as well as carbon and vitamins are vital elements for the growth of microalgae, also determining the biochemical composition of biomass. In this sense, Chapter III presents the study of the influence of different amounts of sodium nitrate (1N = 75 mg L-1; 1.5N = 112.5 mg L-1, and 3N = 225 mg L-1) and phosphate monobasic dehydrate (1P = 5.65 mg L-1, 1.5P = 8.47 mg L-1, and 3P = 16.95 mg L-1) in seawater-based f/2 medium on the growth of Dunaliella salina and ß-carotene biosynthesis, by continuous process with different replenishment proportions (R = 20% and 80%). Best results of cell productivity were obtained by semicontinuous process (mean values of Px up to 6.7 x 104 cells mL-1 d-1 with medium 1N:1P; R =20%) in comparison with batch process cultivation. Maximum cell density (Xm) obtained in this work was not dependent of R, but the best results were obtained when using medium 1.5N:1.5P (mean values up to 5.6 x 105 cells mL-1 with R =80%) instead of 1N:1P. The content of ß-carotene in the cells, in general, was higher in cells grown in medium 1N:1P (mean yield values up to 57.5 mg g-1 with R =80%) in comparison with medium 1.5N:1.5P. The cultivation of D. salina with media 3N:3P led to a long lag phase, followed by decrease in cell density and cell lysis. The use of a tubular photobioreactor contributed to successfully cultivate this microalga without contamination by protozoa. The cultivation of Dunaliella salina in tubular photobioreactor with the use of 12:12 photoperiod was appropriate, as well as to induce carotenogenesis, in the second stage, by increasing the light intensity and absence of pH control

As microalgas, micro-organismos fotossintetizantes, são ricas em lipídios, ácidos graxos poli-insaturados, carboidratos, proteínas, vitaminas, além de carotenoides que são antioxidantes com potencial de proteger o organismo humano de várias doenças incluindo a obesidade, doenças cardiovasculares, doenças relacionadas à visão como a degeneração macular e certos tipos de câncer, entre outras. Esses pigmentos naturais têm aplicações em indústrias farmacêuticas (nutracêuticos), alimentícias (colorantes, alimentos funcionais e suplementos) e de cosméticos (exemplo: filtro solar) e na aquacultura (ração animal). A microalga Dunaliella salina é capaz de sintetizar, sob alta intensidade luminosa e limitação de nutrientes como fontes de fósforo e nitrogênio, dentre outras condições de estresse, 10 % do peso seco em ß-caroteno (pigmento laranja com atividade pró-vitamina A). Assim, neste trabalho, numa primeira etapa, foi feita uma revisão da literatura abordando a produção de carotenoides por microalgas, bem como sua aplicação. Nesse levantamento bibliográfico abordou-se, dentre outros assuntos, as vantagens do cultivo de microalgas em relação as fontes tradicionais (plantas superiores), assim como uma discussão dos diferentes sistemas de cultivos e sua importância no crescimento celular. Esse review apresentou uma análise crítica dos principais regimes operacionais como batch, fed-batch, semicontínuo e contínuo. Apresentou-se também informações relevantes sobre os mais importantes produtores mundiais de carotenoides de microalgas. Numa segunda etapa, foi desenvolvido um método modificado de microextração líquido-líquido dispersivo modificado (DLLME) para a rápida extração de ß-caroteno de Dunaliella salina cultivada em fotobiorreatores tubulares, com subsequente desenvolvimento de método cromatográfico em uma coluna C4 para a separação do isômero geométrico de ß-caroteno. A extração ótima de ß-caroteno foi obtida com benzeno como solvente extrator e água com 50% de acetona como dispersante. Empregando uma fase móvel composta por metanol e água (95:5, v/v) em HPLC, foi possível a detecção/quantificação de ß-caroteno com 14 minutos de tempo de retenção. Além dos tempos curtos de análises (<20 min), pela extração em volume reduzido (< 10 mL resíduos orgânicos) este método obedece aos princípios da química verde. Sabe-se que nitrogênio, fósforo, assim como carbono e vitaminas são elementos vitais para o crescimento das microalgas e também exercem influência na composição bioquímica da biomassa. Assim, na terceira etapa deste trabalho, estudou-se a influência das quantidades de nitrato de sódio (75 mg L-1, denominado 1N; 112,5 mg L-1, denominado 1,5N; 225 mg L-1, denominado 3N) e de fosfato monobásico dihidratado (5,65 mg L-1, denominado 1P; 8,47 mg L-1, denominado 1,5P; 16,95 mg L-1, denominado 3P) em meio f/2, que tem como base a água do mar, no crescimento e na síntese de ß-caroteno da Dunaliella salina por processo semicontínuo, com uso de frações de corte (R) de 20% e 80%. Foram obtidas produtividades celulares mais elevadas em processos semicontínuos do que em processo descontínuo, com produtividades médias de até 6,7 x 104 células mL-1 d-1 (meio 1N:1P; R =20%). A máxima concentração celular (Xm) obtida neste trabalho não foi dependente de R. Os melhores resultados de Xm foram obtidos quando se usou meio 1,5N:1,5P em vez de meio, com 1N:1P, com valores médios de até 5,6 x 105 células m L-1 (R =80%). O conteúdo de ß-caroteno nas células, de maneira geral, foi maior nas células cultivadas em meio 1N:1P do que no meio 1,5N:1,5P, com valores até 57,5 mg g-1 (R =80%). O cultivo de D. salina com o meio 3N:3P levou a uma longa fase lag, seguida por uma diminuição na concentração celular e sua lise. O cultivo de células em um fotobiorreator tubular contribuiu para um crescimento celular sem contaminação por protozoários. O cultivo de Dunaliella salina em fotobiorreator tubular com o uso de fotoperíodo 12:12 foi apropriado, assim como induzir a carotenogênese, no segundo estágio, por meio do aumento da intensidade luminosa e ausência de controle de pH

Validation of a model for ranking aquaculture facilities for risk-based disease surveillance.

A semi-quantitative model for risk ranking of aquaculture facilities in Switzerland with regard to the introduction and spread of Viral Haemorrhagic Septicaemia (VHS) and Infectious Haematopoietic Necrosis (IHN) was developed in a previous study (Diserens et al., 2013). The objective of the present study was to validate this model using data collected during field visits on aquaculture sites in four Swiss cantons compared to data collected through a questionnaire in the previous study. A discrepancy between the values obtained with the two different methods was found in 32.8% of the parameters, resulting in a significant difference (p<0.001) in the risk classification of the facilities. As data gathered exclusively by means of a questionnaire are not of sufficient quality to perform a risk-based surveillance of aquaculture facilities a combination of questionnaires and farm inspections is proposed. A web-based reporting system could be advantageous for the factors which were identified as being more likely to vary over time, in particular for factors considering fish movements, which showed a marginally significant difference in their risk scores (p≥0.1) within a six- month period. Nevertheless, the model proved to be stable over the considered period of time as no substantial fluctuations in the risk categorisation were observed (Kappa agreement of 0.77).Finally, the model proved to be suitable to deliver a reliable risk ranking of Swiss aquaculture facilities according to their risk of getting infected with or spreading of VHS and IHN, as the five facilities that tested positive for these diseases in the last ten years were ranked as medium or high risk. Moreover, because the seven fish farms that were infected with Infectious Pancreatic Necrosis (IPN) during the same period also belonged to the risk categories medium and high, the classification appeared to correlate with the occurrence of this third viral fish disease.

Colorful invasion in permissive Neotropical ecosystems: establishment of ornamental non-native poeciliids of the genera Poecilia/Xiphophorus (Cyprinodontiformes: Poeciliidae) and management alternatives

Headwater creeks are environments susceptible to invasion by non-native fishes. We evaluated the reproduction of 22 populations of the non-native livebearers guppy Poecilia reticulata, black molly Poecilia sphenops, Yucatan molly Poecilia velifera, green swordtail Xiphophorus hellerii, southern platyfish Xiphophorus maculatus, and variable platyfish Xiphophorus variatus during an annual cycle in five headwater creeks located in the largest South American ornamental aquaculture center, Paraíba do Sul River basin, southeastern Brazil. With few exceptions, females of most species were found reproducing (stages 2, 3, 4) all year round in the creeks and gravid females of all species showed small sizes indicating stunting. Juveniles were frequent in all sites. The fecundity of the six poeciliids was always low in all periods. The sex ratio was biased for females in most species, both bimonthly as for the whole period. Water temperature, water level and rainfall were not significantly correlated with reproduction in any species. Therefore, most populations appeared well established. The pertinence of different management actions, such as devices to prevent fish escape, eradication with rotenone and research about negative effects on native species, is discussed in the light of current aquaculture practices in the region.(AU)

Riachos de cabeceira são ambientes susceptíveis à invasão por peixes não-nativos. Neste trabalho, avaliou-se a reprodução de 22 populações dos poecilídeos não-nativos guppy Poecilia reticulata, molinésia preta Poecilia sphenops, molinésia Poecilia velifera, espadinha Xiphophorus hellerii, plati Xiphophorus maculatus e plati variado Xiphophorus variatus durante diferentes anos em cinco riachos de cabeceira localizados no maior polo de piscicultura ornamental da América do Sul, bacia do rio Paraíba do Sul, sudeste do Brasil. Foram encontradas fêmeas da maioria das espécies em reprodução (estágios 2, 3, 4), durante todos os anos nos riachos e fêmeas grávidas de todas as espécies apresentaram pequeno tamanho indicando nanismo. Juvenis de todas as espécies foram frequentes em todos os locais. A fecundidade das seis espécies sempre foi baixa em todos os períodos. Para os períodos bimestrais e totais, encontrou-se mais fêmeas que machos na maioria das espécies. Temperatura e nível de água dos riachos, bem como precipitação pluviométrica não foram correlacionadas com a reprodução. Todas as populações estão estabelecidas nos locais e ações de gerenciamento como dispositivos para impedir a fuga de peixes, erradicação com rotenona e pesquisa científica sobre os efeitos negativos nas espécies nativas são discutidas em relação às práticas de piscicultura na região.(AU)

Freshwater parameters in the state of Rio Grande do Sul, southern Brazil, and their influence on fish distribution and aquaculture

This study analyzed the relationship between several water quality parameters (pH, hardness, alkalinity, turbidity, iron and manganese) levels measured over a 16 year period with fish distribution and aquaculture in the state of Rio Grande do Sul, Southern Brazil. The mean pH values were within a neutral range (6.5-7.5), but the maximum and minimum values reached inappropriate levels for fish farming in some cities. Alkalinity levels were very low (except in the southwest region of the state), which may have contributed to pH variation. Hardness, turbidity, iron (except the region near Caçapava do Sul City) and manganese were within safe ranges for fish farming; however, turbidity levels occasionally increased to levels outside the safe range. In conclusion, the water quality in the Rio Grande do Sul, in general, can be considered adequate for aquaculture, but the fish farmers must be aware of the methods to reduce turbidity, such as the use of calcium sulfate.(AU)

Este estudo analisou a relação entre vários parâmetros de qualidade da água (pH, dureza, alcalinidade, turbidez, ferro e manganês durante 16 anos) com a distribuição de peixes e piscicultura no estado do Rio Grande do Sul, Brasil. O pH ficou em média em uma faixa neutra (6,5-7,5), mas valores máximos e mínimos atingiram níveis não apropriados para a piscicultura em algumas cidades. Os valores de alcalinidade foram baixos (exceto na região sudoeste do estado), o que poderia contribuir para oscilações no pH. Dureza, turbidez, ferro (exceto na região próxima à cidade de Caçapava do Sul) e manganês ficaram dentro de níveis aceitáveis para a piscicultura, mas a turbidez ocasionalmente elevou-se a níveis fora dessa faixa aceitável e os piscicultores devem ter algum mecanismo para reduzi-los. Em conclusão, de forma geral a qualidade da água do Rio Grande do Sul pode ser considerada adequada para a aquicultura, mas os piscicultores devem conhecer métodos para corrigir a turbidez, como a utilização de sulfato de cálcio.(AU)

New approaches for growth improvement in pejerrey Odontesthes bonariensis (Valenciennes, 1835) culture (Atherinomorpha: Atherinopsidae)

The pejerrey is the most important recreational species in shallow temperate lakes and reservoirs of Argentina and the attempts to develop its culture have started a century ago. A common constraint of pejerrey aquaculture is its poor growth under traditional intensive rearing techniques. The aim of this study was to evaluate the possibility to achieve and maintain high growth rates of pejerrey throughout the rearing process by semi-intensive culture method . Four floating cages were installed in La Salada de Monasterio Lake and each one was stocked with 300 juveniles (10.22 ±0.38cm; 6.52 ±0.82g). From January through March all fish were exposed to natural zooplankton as food source, whereas from April to September two cages were supplied daily with artificial food. The fish exposed to artificial supplementary diets exhibited significantly higher growth (17.5 ±0.98cm; 41.05 ±8.55g) than those in the control cages (15.02 ±0cm ; 23.5 ±0.84g), and exceeded the known values in pejerrey culture. The results suggest that the species potential growth is not fully achieved by common intensive methods and it can be improved by semi-intensive techniques. Accordingly a better understanding of the species nutritional requirements is needed to improve growth rates and enhance pejerrey culture.

El pejerrey es la especie de mayor importancia deportiva en lagos someros templados y embalses de Argentina y el desarrollo de su acuicultura data de cien años atrás. Un impedimento común para el desarrollo de la acuicultura del pejerrey es el pobre crecimiento que manifiesta bajo cultivo intensivo. El objetivo de este estudio fue evaluar la posibilidad de alcanzar y mantener altas tasas de crecimiento en el pejerrrey mediante cultivo semi-intensivo. Se instalaron cuatro jaulas flotantes en la laguna La Salada de Monasterio, sembrándose cada una con 300 juveniles (10.22 ±0.38cm; 6.52 ±0.82g). Desde enero hasta marzo los peces se alimentaron con el zooplancton natural de la laguna, mientras que desde abril hasta septiembre dos jaulas fueron suplementadas diariamente con alimento balanceado, dejándose las otras dos como controles. Los peces bajo dietas suplementadas mostraron crecimientos significativamente superiores (17.5 ±0.98cm; 41.05 ±8.55g) a los de las jaulas control (15.02 ±0cm ; 23.5 ±0.84g), excediendo incluso los conocidos en el cultivo de pejerrey en períodos similares. Los resultados obtenidos sugieren que el potencial de crecimiento del pejerrey no está siendo explotado en su totalidad bajo las técnicas de cultivo tradicionales y puede mejorarse mediante el cultivo semi-intensivo. En consecuencia es necesaria una mejor comprensión de los requerimientos nutricionales del pejerrey para incrementar sus tasas de crecimiento y así mejorar su cultivo.

Folk classification of the crabs and swimming crabs (Crustacea-Brachyura) of the Mamanguape river estuary, Northeastern-Brazil.

BACKGROUND: Folk taxonomy is a sub-area of ethnobiology that study the way of how traditional communities classify, identify and name their natural resources. The work present was undertaken in two traditional communities (Barra de Mamanguape and Tramataia). The objective of this study was investigate the ethnobiological classification of the local crabs and swimming crabs used by the crustaceous gatherers of the Mamanguape River Estuary (MRE), Paraíba State, Brazil. METHODS: The methodology used here involved a combination of qualitative methods (open interviews, semi-structured interviews, direct observations, guided tours, surveys, and interviews in synchronic and diachronic situations that crossed-checked and repeated identifications) and quantitative methods (Venn diagram). A total of 32 men and women were interviewed in the two communities. Specimens of the local crustaceans were collected and identified by the harvesters themselves, subsequently fixed in formalin, conserved in 70% ethyl alcohol, identified using appropriate specialized literature, and then deposited in the laboratory of the Zoology Department of the University State of Paraiba. RESULTS: The crustaceous gatherers we studied were observed to group crustaceans according to their similarities and differences, producing a hierarchical classification system containing four levels of decreasing taxonomic order: unique beginner, life-form, generic, and specific. A sequential and/or semantic system classification system that is used to classify the ontogeny of the female swimming crab was also identified.Of the nine folk generics identified, 44.5% were monotypic. 55.5% were polytypic and were subdivided into 15 folk specifics.An identification key was elaborated with the data obtained about the folk polytypics generics. CONCLUSION: The detailed knowledge concerning the crabs and swimming crabs revealed by the MRE crustaceous gatherers demonstrates that these people detain a vast knowledge concerning these marine resources. This local knowledge provides a rich but little-known source of information that will aid future ecological and/or zoological studies in the region that will be indispensable for producing management plans to help guarantee the sustainability of these local natural resources.

Comparación entre lubina (Dicentrarchus labrax) salvaje y cultivada: composición química y variación del contenido en ácidos grasos tras el cocinado / Wild and farmed sea bass (Dicentrarchus labrax) comparison: chemical composition and variations in the fatty acid profi le after cooking

La lubina (Dicentrarchus labrax) es una especie de elevado valor comercial, cuyo cultivo ha experimentadoun considerable incremento en los últimos años. Debido a que el consumidor considera que el productoprocedente de la pesca extractiva es de mayor calidad, el primer objetivo planteado en el presente estudio hasido comparar la composición nutricional de la lubina procedente de pesca extractiva (salvaje) con la de lalubina procedente de la acuicultura (cultivada). Ya que, desde un punto de vista nutricional, el pescado es unimportante fuente de proteínas y de ácidos grasos poliinsaturados de cadena larga ω−3, especialmente ácidoeicosapentanoico (EPA, C20:5 ω−3) y docosahexanoico (DHA, C22:6 ω−3), el segundo objetivo ha sido estudiarlas diferencias en el perfil de ácidos grasos de lubinas de ambas procedencias, y evaluar el efecto delcocinado sobre el mismo. Se seleccionaron 10 especimenes de cada tipo de lubina, con un peso medio de 350 g,para la determinación de la composición química proximal (proteínas, grasa, humedad y cenizas), el contenidode minerales, el nitrógeno básico volátil total, el pH muscular y el contenido de hidroxiprolina y colágeno. Elperfil de ácidos grasos se analizó en la carne de lubina cruda y cocinada al vapor, mediante cromatografía gaseosa.Los resultados obtenidos mostraron diferencias estadísticamente signifi cativas en aquellos parámetros quedependen directamente de la alimentación y el medio ambiente (grasa total y minerales). En cuanto al perfilde ácidos grasos se observaron diferencias en el contenido de ácido linoléico (principal ω−6), mostrando lalubina cultivada una concentración signifi cativamente superior. Aunque no encontramos cambios en el perfilde ácidos grasos de la carne de la lubina salvaje después del cocinado al vapor durante cinco minutos, en la lubina cultivada si se observaron diferencias signifi cativas, como consecuencia de la pérdida de ácidos grasosmonoinsaturados en la grasa ventral durante la cocción

Sea bass (Dicentrarchus labrax) has a high commercial value, and has been widely farmed in the last tenyears. Consumers consider that wild sea bass presents a high quality, so that the first objective of the presentstudy has been to compare the chemical composition of the flesh from wild and farmed sea bass. In addition,from a nutritional point of view, fish meat is considered an important dietary source of protein and long chainω−3 polyunsaturated fatty acids, mainly eicosapentaenoic acid (EPA, C20:5 ω-3) and docosahexaenoic acid(DHA, C22:6 ω-3), because of that the second objective of our work has been to ascertain the fatty acidprofi le in the flesh of wild and farmed sea bass and to evaluate the changes in these nutrients during steamcooking. 10 specimens of each origin (wild and farmed) of sea bass with an average size of 350g, were selectedto determine the proximate composition (protein, fat, moisture and ash), mineral content, total basic volatilenitrogen, muscle pH, and hydroxyproline and collagen concentrations. The fatty acids were determined in theflesh of raw and steam cooked fillets of both types of sea bass using gas chromatography. The obtained resultsshowed statistical differences in those parameters related to environmental and nutritional conditions (total fatand mineral content). The profile of fatty acids showed statistical differences due to type of cultivar since theflesh of farmed sea bass presented the highest content of linoleic acid (the main ω−6). No changes in the fattyacids of wild sea bass flesh after steam coking were observed, however, the flesh of farmed specimens showedsignifi cant losses of monounsaturated fatty acids (oleic acid) from the ventral fat probably from adipose tissuelocated beneath the skin

Evolución del peso económico de la acuicultura marina / Evolution of economic weight of the sea acuiculture

La evolución y crecimiento del sector de la acuicultura marina ha sido continua en los últimos años como respuesta fundamental a la pesca convencional, para incrementar la producción de productos marinos y también para intentar mantener estable la producción pesquera. En este sentido, se describe el sector de la acuicultura marina así como su importancia económica en Murcia fundamentalmente, dentro del marco de España y la U.E. (AU)