Les téléostéens euryhalins peuvent vivre dans des milieux à salinité très différentes. L'objectif de mon travail est de décrire les processus d'acclimatation à l'eau salée chez la truite arc-en-ciel par une étude couplant approches de génomique fonctionnelle et génétique. A partir d'une première approche cinétique de transcriptomie différentielle menée sur la branchie, une liste de gènes candidats a été établie et la réponse physiologique des poissons étudiée. Les principaux résultats révèlent de bonnes capacités d'euryhalinité et une réponse transcriptomique maximum 24h après le transfert en eau de mer. Des processus biologiques impliqués dans les mécanismes d'acclimatation sont également proposés. Une seconde partie de ce travail consistait en la caractérisation d'un contrôle génétique des processus liés à l'acclimatation à l'eau de mer chez la truite. Utilisant comme caractères, les teneurs plasmatiques en sodium et en chlore mesurées 24h après un transfert d'eau douce en eau salée répété à 2 reprises, ainsi que le poids branchial, des analyses univariées et multivariées ont permis de détecter 18 QTL dont 9 sont qualifiés de robustes. Une dernière étape de détection de QTL d'expression a alors permis de proposer 69 gènes candidats de premier choix. C'est la première fois qu'une approche mêlant transcriptomie différentielle et approche QTL / eQTL est menée chez une espèce d'intérêt aquacole au génome non séquencé pour la capacité d'acclimatation à un milieu osmotique différent. Ces résultats pavent la route pour une investigation précise des bases génétiques des processus d'acclimatation à l'eau de mer chez les téléostéens.

Transcriptomics and gene expression profiling enables the elucidation of the genetic response of an organism to various environmental cues. Transcriptomics enables the deciphering of differences between two closely related organisms to the same environment and in contrast, enables the elucidation of genetic responses of the same organism to different environmental cues. Two major methods are utilized for the study of transcriptomes, high-throughput sequencing and microarray analysis. High-throughput sequencing technologies such as the Illumina platform are relatively new and protocols must be developed for the analyses of transcriptomes (RNA-sequencing). A RNA-seq protocol was developed and refined for the Illumina sequencing platform. This protocol was then utilized for the de novo sequencing of the steelhead salmon transcriptome. Hatchery steelhead exhibit a reduced fitness compared to wild steelhead that has been shown to be genetically based. Consequently, the steelhead transcriptome was assembled, annotated, and used to identify gene expression differences between hatchery and wild fish. We uncovered many differentially expressed genes involved in metabolic processes and growth and development. This work has created a better understanding of the genetic differences between hatchery and wild steelhead salmon. Brachypodium distachyon is a monocot grass important as a model for cereal crops and potential biofuels feedstocks. To better understand the genetic response of this plant to different environmental cues, a comprehensive assessment of the transcriptomic response was conducted under a variety of conditions including diurnal/circadian light/dark/temperature environments and different abiotic stress conditions. Using a whole-genome tiling DNA microarray, we identified that the majority of transcripts in Brachypodium exhibit a daily rhythm in their abundance that is conserved between rice and Brachypodium. We also identified numerous cis-regulatory elements dictating these rhythmic expression patterns. We also identified the genetic response to abiotic stresses such as salinity, drought, cold, heat, and high light. We uncovered a core set of genes which responds to all stresses, indicating a core stress response. A large number of transcription factors were uncovered as potential nodes for regulating the abiotic stress response in Brachypodium. Moreover, promoter elements that drive specific responses to discrete abiotic stresses were uncovered. Altogether, the transcriptome analyses in this work furthers our understandings of how particular organisms respond to environmental cues and better elucidates the relationship between genes and the environment. / Graduation date: 2012 / Access restricted to the OSU Community at author's request from Oct. 5, 2011 - April 5, 2012.

Thesis (Ph.D. (Zoology))--North-West University, Potchefstroom Campus, 2005.

Thesis (Ph.D. (Zoology))--North-West University, Potchefstroom Campus, 2005

Thesis (Ph.D. (Zoology))--North-West University, Potchefstroom Campus, 2005

Diss. (sammanfattning) Umeå : Sveriges lantbruksuniv., 2003. / Härtill 5 uppsatser.

This diploma thesis was focused on the possibilities of extending the shelf-life of fish products by dipping containing seven commercial additives. ANTIBAK, MIC STAB, Bakont, SEA-F75, Misocarine LR, SAFE A Plus and AMX liquid. The effectiveness of these substances on the extending of shelf-life was evaluated on the basis of tests of TVC (total viable count), level of fat and protein oxidation, determination of nutritional parameters of muscle, and finaly sensory analysis. Experimental species were 2 important commodities for the Czech aquaculture rainbow trout (Oncorhynchus mykiss) and common carp (Cyprinus carpio). The project was divided into 6 sub-stages. During testing was the initial number of aditives (7) limited by stepwise selection for 2 preparations. Namely Bakont and AMX liquid, which were tested further on trout (filet with skin and scales) and carp (filets with skin without scales) chilled bulk and chilled packaged under vakuum. For trout was studied antimicrobial effect of dipping on eviscerated fish with the head with- or without gills. Treated trout fillets in bulk and vakuum-packed showed significantly less abundance of muscle mikroflora. In the case of carp fillets chilled bulk we can not say that the bath had influence on the CMP in meat. However, the combination of dipping and vakuum packaging was singnificantly different between the control and product Bakont. AMX liquid was not applied in this case in sufficient dose or in sufficient time to carp muscle. A positive finding is that the application of the aditives to the product "eviscerated trout with head" it does not matter, whether the gills are left in fish or not. However, in all cases the analysis of the presence of pathogens Escherichia coli, Salmonella spp. or Listeria monocytogenes were negative. From the results of sensory analysis can be concluded, that the substances contained in aditives are not reflected in the sensory properties of tested fish.

The objective of this thesis was to test the environmental friendly additive substance, in particular sodium caseinate, which is not subject to designation "E" on the label of the product, which is unpopular among the consumers, and which would provide so-called a "higher value" to a product of economically important fish species in the Czech Republic, specifically the common carp (Cyprinus carpio), silver carp (Hypophthalmichthys molitrix) and the rainbow trout (Oncorhynchus mykiss).Determination of the influence of this additive on microbial and biochemical processes, and also on organoleptic properties of the selected smoked fish was another goal of the work. Three concentrations of this product were used for application in total, in particular 25, 50 and 100 g×kg-1. The results of this work confirmed that, due to caseinate (concentration of 100 g×kg-1) such losses of water were avoided, as observed in case of the control group, to which no additive product was applied, and which served for comparison with the groups treated with caseinate. General carp had an average loss of 12.9 % for the samples treated with sodium caseinate and 14 % for the control group. The silver carp white showed similar results. The group treated with caseinate lost 12.4 % in average, and the control group of approximately 14 %. The best results were recorded with the rainbow trout, which, due to caseinate withheld the largest amount of water, respectively, it did not lose so much of weight, in particular 15.9 % for sodium caseinate compared to 19.3 % measured in the control group, however these differences were not confirmed as statistically conclusive. As for the texture of the meat, tougher samples came out for the ones treated with sodium caseinate compared to the more brittle control group. In carp and trout no statistically noteworthy dissimilarity in stiffness of meat was proved between the control group and the group with the applied additive product. While these differences were significant in silver carp. While for silver carp were these differences significant. The control group showed clearly (p<0.05) lower stiffness compared to the group, to which the additive product was applied. Microbiological analysis was performed on the 7th day after smoking, and the values were in the range of 2×10 to 1.9×10^2 CFU×g-1. In the experiment, groups of test fish species did not show any statistically significant difference (p>0.05). Tests for the possible presence of Listeria monocytogenes in all of the smoked fish samples and the control group were negative. Nutrient composition was mainly focused on the basic nutrient components, which were the proteins, fats and carbohydrates. The control group did not show any significant differences compared to the group to which sodium caseinate was applied. The results from the consumers and sensory analysis by a panel of trained persons were very similar. No statistically significant differences between the group treated with caseinate sodium, and the untreated so called control group of smoked species of fish.

The aim of this thesis was to assess the effects of long-term nitrite exposure on mortality, growth rate and blood biochemistry in rainbow trout (Oncorhynchus mykiss). Furthermore, acute toxicity tests with nitrite were performed on rainbow trout (Oncorhynchus mykiss) and sheatfish (Silurus glanis). The theoretical part focuses on aquatic toxicology including toxicity evaluation of substances and preparations for water organisms. Detailed information on nitrite are summarized there, namely information on nitrite occurrence and sources in aquatic environment and the mechanism of their uptake and toxic influence on fish including factors influencing their toxicity. The practical part consists of methodology and results of acute toxicity tests on rainbow trout and sheatfish and sub-chronic test on rainbow trout. According to the acute toxicity tests results, 96hLC50 values were estimated at 11.2 mg.l-1 NO2- for rainbow trout and 15.3 mg.l-1 NO2- for sheatfish. Sub-chronic exposure of rainbow trout to nitrite concentrations ranging from 0.01 to 3.0 mg.l-1 lasting 28 days caused an increase of glucose concentration and a decrease of potassium concentration in the blood plasma among all experimental fish compared to control. Elevated nitrite levels were found in the plasma of the fish exposed to concentrations of 0.6 mg.l-1 NO2- and greater. The plasma nitrite levels did not reach those applied in any experimental group in the present study. At highest nitrite concentration (3.0 mg.l-1 NO2-), 42 % growth inhibition and 65 % mortality among fish was noticed. On the basis of growth rate inhibition data, the values of NOEC and LOEC were estimated at 0.01 mg.l-1 and 0.2 mg.l-1 NO2-, respectively.

Examination of variation at polymorphic microsatellite loci is a widely accepted method for determining parentage and examining genetic diversity within rainbow trout (Oncorhynchus mykiss) breeding programs. Genotyping costs are considerable; therefore, we developed a single-step method of co-amplifying twelve microsatellite loci in two hexaplex reactions. The protocol is explicitly described to ensure reproducible results. I applied the protocol to samples previously analyzed at the National Center for Cool and Coldwater Aquaculture (NCCCWA) with previously reported marker sets for a comparison of results. Each marker within the multiplex system was evaluated for duplication, null alleles, physical linkage, and probability of genotyping errors. Data from four of the 12 markers were excluded from parental analysis based on these criteria. Parental assignments were compared to those of a previous study that used five independently amplified microsatellites. Percentages of progeny assigned to parents were higher using the subset of eight markers from the multiplex system than with five markers used in the previous study (98% vs. 92%). Through multiplexing, use of additional markers improved parental allocation while also improving efficiency by reducing the number of PCR reactions and genotyping runs required. I evaluated the methods further through estimation of F-statistics, pairwise genetic distances, and cluster analysis among brood-years at the NCCCWA facility. These estimates were compared to those from nine independently amplified microsatellites used in a previous study. Fst metrics calculated between brood-years showed similar values of genetic differentiation using both marker sets. Estimates of individual pairwise genetic distances were used for constructing neighbor-joining trees. Both marker-sets yielded trees that showed similar subpopulation structuring and agreed with results from a model-based cluster analysis and available pedigree information. These approaches for detecting population substructure and admixture portions within individuals are particularly useful for new breeding programs where the founders' relatedness is unknown. The 2005 NCCCWA brood-year (75 full-sib families) was challenged with Flavobacterium psychrophilum, the causative agent of bacterial coldwater disease (BCWD). The overall mortality rate was 70%, with large variation among families. Resistance to the disease was assessed by monitoring post-challenge days-to-death. Phenotypic variation and additive genetic variation were estimated using mixed models of survival analysis. The microsatellite markers used were previously isolated from BAC clones that harbor genes of interest and mapped onto the rainbow trout genetic linkage map. A general relationship between UBA gene sequence types and MH-IA-linked microsatellite alleles indicated that microsatellites mapped near or within specific major histocompatibility (MH) loci reliably mark sequence variation at MH genes. The parents and grandparents of the 2005 brood-year families were genotyped with markers linked to the four MH genomic regions (MH-IA, MH-IB, TAP1, and MH-II) to assess linkage disequilibrium (LD) between those genomic regions and resistance to BCWD. Family analysis suggested that MH-IB and MH-II markers are linked to BCWD survivability. Tests for disease association at the population level substantiated the involvement of MH-IB with disease resistance. The impact of MH sequence variation on selective breeding for disease resistance is discussed in the context of aquaculture production. / Master of Science