BackgroundTo enhance capabilities for genomic analyses in rainbow trout, such as genomic selection, a large suite of polymorphic markers that are amenable to high-throughput genotyping protocols must be identified. Expressed Sequence Tags (ESTs) have been used for single nucleotide polymorphism (SNP) discovery in salmonids. In those strategies, the salmonid semi-tetraploid genomes often led to assemblies of paralogous sequences and therefore resulted in a high rate of false positive SNP identification. Sequencing genomic DNA using primers identified from ESTs proved to be an effective but time consuming methodology of SNP identification in rainbow trout, therefore not suitable for high throughput SNP discovery. In this study, we employed a high-throughput strategy that used pyrosequencing technology to generate data from a reduced representation library constructed with genomic DNA pooled from 96 unrelated rainbow trout that represent the National Center for Cool and Cold Water Aquaculture (NCCCWA) broodstock population.ResultsThe reduced representation library consisted of 440 bp fragments resulting from complete digestion with the restriction enzyme HaeIII; sequencing produced 2,000,000 reads providing an average 6 fold coverage of the estimated 150,000 unique genomic restriction fragments (300,000 fragment ends). Three independent data analyses identified 22,022 to 47,128 putative SNPs on 13,140 to 24,627 independent contigs. A set of 384 putative SNPs, randomly selected from the sets produced by the three analyses were genotyped on individual fish to determine the validation rate of putative SNPs among analyses, distinguish apparent SNPs that actually represent paralogous loci in the tetraploid genome, examine Mendelian segregation, and place the validated SNPs on the rainbow trout linkage map. Approximately 48% (183) of the putative SNPs were validated; 167 markers were successfully incorporated into the rainbow trout linkage map. In addition, 2% of the sequences from the validated markers were associated with rainbow trout transcripts.ConclusionThe use of reduced representation libraries and pyrosequencing technology proved to be an effective strategy for the discovery of a high number of putative SNPs in rainbow trout; however, modifications to the technique to decrease the false discovery rate resulting from the evolutionary recent genome duplication would be desirable.

BackgroundFish under intensive culture conditions are exposed to a variety of acute and chronic stressors, including high rearing densities, sub-optimal water quality, and severe thermal fluctuations. Such stressors are inherent in aquaculture production and can induce physiological responses with adverse effects on traits important to producers and consumers, including those associated with growth, nutrition, reproduction, immune response, and fillet quality. Understanding and monitoring the biological mechanisms underlying stress responses will facilitate alleviating their negative effects through selective breeding and changes in management practices, resulting in improved animal welfare and production efficiency.ResultsPhysiological responses to five treatments associated with stress were characterized by measuring plasma lysozyme activity, glucose, lactate, chloride, and cortisol concentrations, in addition to stress-associated transcripts by quantitative PCR. Results indicate that the fish had significant stressor-specific changes in their physiological conditions. Sequencing of a pooled normalized transcriptome library created from gill, brain, liver, spleen, kidney and muscle RNA of control and stressed fish produced 3,160,306 expressed sequence tags which were assembled and annotated. SNP discovery resulted in identification of ~58,000 putative single nucleotide polymorphisms including 24,479 which were predicted to fall within exons. Of these, 4907 were predicted to occupy the first position of a codon and 4110 the second, increasing the probability to impact amino acid sequence variation and potentially gene function.ConclusionWe have generated and characterized a reference transcriptome for rainbow trout that represents multiple tissues responding to multiple stressors common to aquaculture production environments. This resource compliments existing public transcriptome data and will facilitate approaches aiming to evaluate gene expression associated with stress in this species.

Studies were carried out to investigate the effect of temperature, salinity, ammonia, nitrite and nitrate on food consumption of pink shrimp Farfantepenaeus paulensis. Juveniles (0.2 - 0.4 g) were acclimated for 15 days in seawater with different temperatures, salinities and concentrations of ammonia, nitrite and nitrate. After the acclimation period, 20 shrimps per treatment were individualized in order to have their ration intake analyzed through the amount of ration offered and left over within a 24-hour period. Mean food consumption presented significant alterations (P<0.05) for the tested temperatures and nitrite concentrations, whereas for the salinity, ammonia and nitrate treatments, shrimp presented no alteration on food intake (P>0.05). According to the results obtained, temperature and nitrite affected F. paulensis food consumption. On the other hand, variables as salinity, ammonia and nitrate did not affect shrimp appetite. However, the possibility of this to happen over long periods, prejudicing the species culture in captivity, reinforced the necessity of regular water quality management.
Nos cultivos de organismos aquáticos, a manutenção da qualidade da água é fundamental para o sucesso da atividade, tendo em vista que variações nos parâmetros físico-químicos implicam em alterações metabólicas. O consumo de alimento por parte dos camarões pode ser afetado por estas variações, o que interfere nas taxas de crescimento e conseqüentemente na biomassa final produzida. O objetivo deste trabalho foi investigar o efeito da temperatura, salinidade, amônia, nitrito e nitrato sobre o consumo alimentar do camarão-rosa Farfantepenaeus paulensis. Desta forma, juvenis (0,2-0,4 g) foram aclimatados por 15 dias em água do mar com diferentes temperaturas, salinidades, concentrações de amônia, nitrito e nitrato. Após o período de aclimatação, 20 camarões de cada tratamento foram individualmente analisados para observar a relação entre a quantidade de alimento oferecido e a quantidade de alimento ingerido, em um período de 24 horas. O consumo médio apresentou alterações significativas (p<0,05) nos testes de temperatura e de nitrito, enquanto que nos tratamentos de amônia, nitrato e salinidade, não detectou-se alterações no consumo alimentar (p>0,05). De acordo com os resultados obtidos, conclui-se que a temperatura e o nitrito afetam o consumo alimentar de F. paulensis. Por outro lado, para os intervalos testados nos tratamentos de salinidade, amônia e nitrato, a ingestão de alimento dos camarões não foi afetada. Cabe ressaltar que longos períodos de exposição, a estas condições, podem afetar as espécies cultivadas, reforçando a importância do manejo na manutenção da qualidade de água

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The aim of this study was to evaluate the effects of temperature on survival and growth of juvenile marine pejerrey, Odontesthes argentinensis. Juveniles were randomly distributed into plastic tanks (100 L) with 50 juveniles per tank. The growth experiment was carried out at four temperatures: 20, 23, 26, and 29 C with triplicate tanks for each treatment. Survival was not affected in the range of 20-26 C, but it was significantly reduced at 29 C. Pejerrey reared at 23 C showed significantly higher total length compared with the other treatments. Fish maintained at 29 C grew significantly slower than fish reared at all other temperatures, while weight of pejerrey reared at either 20 or 26 C did not differ after 28 d (P > 0.05); they were both significantly smaller than fish kept at 23 C (P < 0.05). Feed consumption increased significantly from 20 to 29 C. The relationships between specific growth rate and temperature, and feed conversion ratio and temperature were adequately fitted with a second-order polynomial equation. The results of this study show that juvenile pejerrey should be reared at around 23 C to maximize growth and food conversion. Björnsson, B., A. Steirnasson, and M. Oddgeirsson. 2001. Optimal temperature for growth and feed conversion of immature cod (Gadus morhua L.). ICES Literature Cited