The aim was to develop new methods for measuring texture of Atlantic salmon (Salmo salar L.) fillets and investigate the genetic basis of flesh quality traits. Firstly, a new tensile strength method was developed to quantify the force required to tear a standardized block of salmon muscle with the aim of identifying those samples more prone to factory downgrading as a result of gaping. The repeatability, sensitivity and predictability of the new technique was evaluated against other common instrumental texture measurement methods. Data from the new method were shown to have the strongest correlations with gaping severity r=-0.514, P<0.001) and the highest level of repeatability of data when analysing cold-smoked samples. The Warner Bratzler shear method gave the most repeatable data from fresh samples and had the highest correlations between fresh and smoked product from the same fish (r=0.811, P<0.001). It is therefore recommended that the new method be adopted for measuring gaping potential and the Warner Bratzler method become the standard for firmness assessment. Genes associated with post mortem softening in mammals were characterised in Atlantic salmon. A previously unknown ancient paralogue of calpastatin (here named CAST2) was identified. Evidence was provided for the existence of highly homologous recent paralogues of CAST2 and CTSD1. Evidence for the ancestral history of these paralogues was provided by phylogenetic analysis. Recent gene duplicates of 6 further genes were identified. In all cases, homology between recent paralogues was greater than 94%. Analysis of synonymous vs non-synonymous nucleotide substitution between the observed paralogue pairs shows a significant purifying selection in most cases. The CTSD1 gene shows significant purifying selection in a pairwise analysis between 12 teleost species (all cases P<0.0001) but a similar analysis of CTSD2 revealed no significant occurrence of purifying selection. The present study provides further support for the idea of asymmetrical selective pressure on paralogues. Genetic markers were developed that can distinguish individuals with above average fillet yield and texture. A database of firmness, tensile strength and fillet yield was made from 254 individuals from 5 batches of farmed salmon and these fish were genotyped at 7 novel SNP loci. Individuals with the combined favourable genotype at CAPN1a and MYOD1b were associated with an average increase in fillet yield of 2.7% above batch average. A combined genotype of CAPN1a, MYOD1b and MYF5 was significantly associated with an average increase in tensile strength of 9.8% above batch average (P=0.015). In both cases individuals with the combined favourable genotype occurred with a frequency of c. 6% across all batches. The favourable genotypes had no unfavourable effects on other traits. Highly polymorphic microsatellite loci were used to perform tests of assignment, which revealed an overall correct assignment rate of 92.7% to batch of origin and a minimum reference sample number of 25 was empirically determined. A phylogenetic analysis supported the results of the assignment tests. Given that 7 microsatellites is a relatively small number for a study of this nature, these results suggest that reliable assignment of unknown fish to the true batch of origin is potentially rapid and cost effective. Overall, the thesis presents molecular markers for broodstock selection, new genes of relevance to flesh quality, a new method of texture analysis and a proposal for an escapee traceability project.

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Introduction : La Vitamine A (rétinol, ROL) et son métabolite l’acide rétinoïque (AR) sont essentielles pour l’embryogénèse. L’excès comme l’insuffisance d’AR sont nocives. L’AR est régularisé dans l’embryon par des gènes spécifiques (ALDH, CRABP, CYP). Hypothèse : Les grandes variations d’AR dans le plasma des adultes normaux, nous ont orienté à mesurer les rétinoïdes (ROL et RA) dans le sang de cordon ombilical, pour évaluer des corrélations avec des polymorphismes des gènes impliquées dans le métabolisme de l’AR et le développement rénal-(RALDH2, CRABP2, CYP26A1; B1). Vérifier pour des corrélations entre ces rétinoïdes et/ou avec la taille de reins à la naissance. Méthodes : Extraction du ROL et RA du sang de cordon ombilical de 145 enfants et analyse par HPLC. Le volume des reins a été mesuré par ultrasonographie et l’ADN génomique leucocytaire extrait (FlexiGene DNA-Kit). 10 échantillons d’ADN ont été exclus (qualité). Les htSNP : ALDH1A2, CRABP2, CYP26A1;B1 du génome humain (HapMap) ont été séquencés et génotypés (Sequenom iPlex PCR).Des testes bio-statistiques des fréquences génotypiques et alléliques ont été effectués (Single-Locus, χ2, Kruskal-Wallis, Allelic-Exact).Des corrélations (ROL, RA, SNPs, V-reins) ont été analysés (Kendall-tau /Oakes). Résultats : La Δ RA (0.07-550.27 nmol/l) non corrélé avec la Δ ROL (51.39-3892.70 nmol/l). Il n’y a pas d’association ROL ou RA avec les volumes des reins ou avec les SNPs/ CYP21A1;B1. Corrélations trouvées : 1. (p=0.035), polymorphisme génétique ALDH1A2-SNP (rs12591551:A/C) hétérozygote/CA, (25enfants, 19%) avec moyennes d’AR (62.21nmol/l). 2. (p=0.013), polymorphisme CRABP2-SNP (rs12724719:A/G) homozygote/AA (4 enfants, 3%) avec hautes valeurs moyennes d’AR (141,3 nmol/l). Discussion-Conclusion : Les grandes ΔRA suggèrent une variabilité génique individuelle du métabolisme de ROL. Les génotypes (CA)-ALDH1A2/ SNP (rs12591551:A/C) et (AA) -CRABP2/SNP (rs12724719:A/G) sont associés à des valeurs moyennes hautes d’AR, pouvant protéger l’embryogénèse lors d’une hypovitaminose A maternelle. / Introduction: Vitamin A (retinol, ROL) modulate the embryogenesis thorough RA, its metabolite. Excess or deficiency being pathologic, the RA is tight regulated in the embryo thorough specific genes (ALDH, CRABP, CYP, etc.) important for Vitamin A metabolism. Hypothesis: High RA variations in healthy adults plasma, oriented to ROL, RA evaluation in human cord blood, in regard of possible correlations with polymorphisms of genes involved in RA metabolism and kidney development (RALDH2, CRABP2, CYP26A1,B1). Correlations between ROL and RA and/or with birth kidney size might also occur. Methods: Cord blood ROL and RA were extracted and HPLC analysed, from 145 Montreal healthy newborns. Kidney volumes already measured by ultrasonography. Genomic leucocytary DNA extraction was performed with FlexiGene DNA-Kit. 10 samples excluded (DNA quality). htSNP choices: ALDH1A2, CRABP2, CYP26A1;B1 were made on HapMap human genome. Sequencing, genotyping (Sequenom iPlex PCR) was made for these genes eventual SNPs. Biostatistics tests for genotype and allelic frequencies (Single-Locus, χ2, Kruskal-Wallis, Allelic-Exact) and Kendall-tau /Oakes analysis for eventual ROL, RA, SNPs, V-reins correlations, were performed. Results: No correlation found between Δ RA (0.07-550.27 nmol/L) and Δ ROL (51.39-3892.70 nmol/L). No association ROL or RA with kidney volumes nor with SNPs/ CYP21A1;B1. Found correlations: 1. (p=0.035), polymorphism ALDH1A2-SNP (rs12591551:A/C) heterozygous/CA, (25babies, 19%) with RA (mean ~62.21nmol/L). 2. (p=0.013), polymorphism CRABP2-SNP (rs12724719: A/G) homozygous/AA (4babies, 3%) with RA (mean~141, 3 nmol/L). Discussion/Conclusion: Big Δ RA not correlated with Δ ROL suggests individual genetic variance on RA metabolism. Genotypes (CA)-ALDH1A2/SNP (rs12591551:A/C) and (AA)-CRABP2/SNP (rs12724719: A/G) are associated with high cord blood RA mean and may be embryogenesis protective in a maternal hypovitaminosis-A, environment.

RÉSUMÉ: Introduction : La Vitamine A (rétinol, ROL) et son métabolite l’acide rétinoïque (AR) sont essentielles pour l’embryogénèse. L’excès comme l’insuffisance d’AR sont nocives. L’AR est régularisé dans l’embryon par des gènes spécifiques (ALDH, CRABP, CYP). Hypothèse : Les grandes variations d’AR dans le plasma des adultes normaux, nous ont orienté à mesurer les rétinoïdes (ROL et RA) dans le sang de cordon ombilical, pour évaluer des corrélations avec des polymorphismes des gènes impliquées dans le métabolisme de l’AR et le développement rénal-(RALDH2, CRABP2, CYP26A1; B1). Vérifier pour des corrélations entre ces rétinoïdes et/ou avec la taille de reins à la naissance. Méthodes : Extraction du ROL et RA du sang de cordon ombilical de 145 enfants et analyse par HPLC. Le volume des reins a été mesuré par ultrasonographie et l’ADN génomique leucocytaire extrait (FlexiGene DNA-Kit). 10 échantillons d’ADN ont été exclus (qualité). Les htSNP : ALDH1A2, CRABP2, CYP26A1;B1 du génome humain (HapMap) ont été séquencés et génotypés (Sequenom iPlex PCR).Des testes bio-statistiques des fréquences génotypiques et alléliques ont été effectués (Single-Locus, χ2, Kruskal-Wallis, Allelic-Exact).Des corrélations (ROL, RA, SNPs, V-reins) ont été analysés (Kendall-tau /Oakes). Résultats : La Δ RA (0.07-550.27 nmol/l) non corrélé avec la Δ ROL (51.39-3892.70 nmol/l). Il n’y a pas d’association ROL ou RA avec les volumes des reins ou avec les SNPs/ CYP21A1;B1. Corrélations trouvées : 1. (p=0.035), polymorphisme génétique ALDH1A2-SNP (rs12591551:A/C) hétérozygote/CA, (25enfants, 19%) avec moyennes d’AR (62.21nmol/l). 2. (p=0.013), polymorphisme CRABP2-SNP (rs12724719:A/G) homozygote/AA (4 enfants, 3%) avec hautes valeurs moyennes d’AR (141,3 nmol/l). Discussion-Conclusion : Les grandes ΔRA suggèrent une variabilité génique individuelle du métabolisme de ROL. Les génotypes (CA)-ALDH1A2/ SNP (rs12591551:A/C) et (AA) -CRABP2/SNP (rs12724719:A/G) sont associés à des valeurs moyennes hautes d’AR, pouvant protéger l’embryogénèse lors d’une hypovitaminose A maternelle. Mots clé: sang de cordon ombilical, ROL-rétinol, AR-acide rétinoïque, HPLC, SNP- polymorphisme, ALDH1A2, CRABP2, CYP26A1,développement rénal,embryogénèse. / ABSTRACT Introduction: Vitamin A (retinol, ROL) modulate the embryogenesis thorough RA, its metabolite. Excess or deficiency being pathologic, the RA is tight regulated in the embryo thorough specific genes (ALDH, CRABP, CYP, etc.) important for Vitamin A metabolism. Hypothesis: High RA variations in healthy adults plasma, oriented to ROL, RA evaluation in human cord blood, in regard of possible correlations with polymorphisms of genes involved in RA metabolism and kidney development (RALDH2, CRABP2, CYP26A1,B1). Correlations between ROL and RA and/or with birth kidney size might also occur. Methods: Cord blood ROL and RA were extracted and HPLC analysed, from 145 Montreal healthy newborns. Kidney volumes already measured by ultrasonography. Genomic leucocytary DNA extraction was performed with FlexiGene DNA-Kit. 10 samples excluded (DNA quality). htSNP choices: ALDH1A2, CRABP2, CYP26A1;B1 were made on HapMap human genome. Sequencing, genotyping (Sequenom iPlex PCR) was made for these genes eventual SNPs. Biostatistics tests for genotype and allelic frequencies (Single-Locus, χ2, Kruskal-Wallis, Allelic-Exact) and Kendall-tau /Oakes analysis for eventual ROL, RA, SNPs, V-reins correlations, were performed. Results: No correlation found between Δ RA (0.07-550.27 nmol/L) and Δ ROL (51.39-3892.70 nmol/L). No association ROL or RA with kidney volumes nor with SNPs/ CYP21A1;B1. Found correlations: 1. (p=0.035), polymorphism ALDH1A2-SNP (rs12591551:A/C) heterozygous/CA, (25babies, 19%) with RA (mean ~62.21nmol/L). 2. (p=0.013), polymorphism CRABP2-SNP (rs12724719: A/G) homozygous/AA (4babies, 3%) with RA (mean~141, 3 nmol/L). Discussion/Conclusion: Big Δ RA not correlated with Δ ROL suggests individual genetic variance on RA metabolism. Genotypes (CA)-ALDH1A2/SNP (rs12591551:A/C) and (AA)-CRABP2/SNP (rs12724719: A/G) are associated with high cord blood RA mean and may be embryogenesis protective in a maternal hypovitaminosis-A, environment. Key words: umbilical cord blood, ROL-retinol, AR-retinoic acid, HPLC, SNP- polymorphism, ALDH1A2, CRABP2, CYP26A1,kidney development,embryogenesis. / Note d'excellence 10%: « Le Jury, à l'unanimité, juge ce mémoire excellent et le classe parmi les 10% des mémoires de la discipline » - selon le Rapport définitif du jury d'éxamen d'un mémoire de maîtrise.