A synthetic rainbow trout linkage map provides new insights into the salmonid whole genome duplication and the conservation of synteny among teleosts

<p>Abstract</p> <p>Background</p> <p>Rainbow trout is an economically important fish and a suitable experimental organism in many fields of biology including genome evolution, owing to the occurrence of a salmonid specific whole-genome duplication (4^thWGD). Rainbow trout is among some of the most studied teleosts and has benefited from substantial efforts to develop genomic resources (e.g., linkage maps. Here, we first generated a synthetic map by merging segregation data files derived from three independent linkage maps. Then, we used it to evaluate genome conservation between rainbow trout and three teleost models, medaka, stickleback and zebrafish and to further investigate the extent of the 4^thWGD in trout genome.</p> <p>Results</p> <p>The INRA linkage map was updated by adding 211 new markers. After standardization of marker names, consistency of marker assignment to linkage groups and marker orders was checked across the three different data sets and only loci showing consistent location over all or almost all of the data sets were kept. This resulted in a synthetic map consisting of 2226 markers and 29 linkage groups spanning over 3600 cM. Blastn searches against medaka, stickleback, and zebrafish genomic databases resulted in 778, 824 and 730 significant hits respectively while blastx searches yielded 505, 513 and 510 significant hits. Homology search results revealed that, for most rainbow trout chromosomes, large syntenic regions encompassing nearly whole chromosome arms have been conserved between rainbow trout and its closest models, medaka and stickleback. Large conserved syntenies were also found between the genomes of rainbow trout and the reconstructed teleost ancestor. These syntenies consolidated the known homeologous affinities between rainbow trout chromosomes due to the 4^thWGD and suggested new ones.</p> <p>Conclusions</p> <p>The synthetic map constructed herein further highlights the stability of the teleost genome over long evolutionary time scales. This map can be easily extended by incorporating new data sets and should help future rainbow trout whole genome sequence assembly. Finally, the persistence of large conserved syntenies across teleosts should facilitate the identification of candidate genes through comparative mapping, even if the occurrence of intra-chromosomal micro-rearrangement may hinder the accurate prediction their genomic location.</p

A Type I and Type II microsatellite linkage map of Rainbow trout (Oncorhynchus mykiss) with presumptive coverage of all chromosome arms

BACKGROUND: The development of large genomic resources has become a prerequisite to elucidate the wide-scale evolution of genomes and the molecular basis of complex traits. Linkage maps represent a first level of integration and utilization of such resources and the primary framework for molecular analyses of quantitative traits. Previously published linkage maps have already outlined the main peculiarities of the rainbow trout meiosis and a correspondance between linkage groups and chromosome arms has been recently established using fluorescent in situ hybridization. The number of chromosome arms which were covered by these maps remained unknown. RESULTS: We report an updated linkage map based on segregation analysis of more than nine hundred microsatellite markers in two doubled haploid gynogenetic lines. These markers segregated into 31 linkage groups spanning an approximate total map length of 2750 cM. Centromeres were mapped for all the linkage groups using meiogenetic lines. For each of the 31 linkage groups, the meta or acrocentric structure infered from centromere mapping was identical with those recently found with fluorescent in situ hybridization results. The present map is therefore assumed to cover the 52 chromosome arms which constitute the rainbow trout karyotype. Our data confirm the occurrence of a high interference level in this species. Homeologous regions were identified in eleven linkage groups, reflecting the tetraploid nature of the salmonid genome. The data supported the assumption that gene orders are conserved between duplicated groups and that each group is located on a single chromosome arm. Overall, a high congruence with already published rainbow trout linkage maps was found for both gene syntenies and orders. CONCLUSION: This new map is likely to cover the whole set of chromosome arms and should provide a useful framework to integrate existing or forthcoming rainbow trout linkage maps and other genomic resources. Since very large numbers of EST containing microsatellite sequences are available in databases, it becomes feasible to construct high-density linkage maps localizing known genes. This will facilitate comparative mapping and, eventually, identification of candidate genes in QTL studies

Quantitative trait loci for resistance to Flavobacterium psychrophilum in rainbow trout: effect of the mode of infection and evidence of epistatic interactions.

BACKGROUND: Bacterial cold-water disease, which is caused by Flavobacterium psychrophilum, is one of the major diseases that affect rainbow trout (Oncorhynchus mykiss) and a primary concern for trout farming. Better knowledge of the genetic basis of resistance to F. psychrophilum would help to implement this trait in selection schemes and to investigate the immune mechanisms associated with resistance. Various studies have revealed that skin and mucus may contribute to response to infection. However, previous quantitative trait loci (QTL) studies were conducted by using injection as the route of infection. Immersion challenge, which is assumed to mimic natural infection by F. psychrophilum more closely, may reveal different defence mechanisms. RESULTS: Two isogenic lines of rainbow trout with contrasting susceptibilities to F. psychrophilum were crossed to produce doubled haploid F2 progeny. Fish were infected with F. psychrophilum either by intramuscular injection (115 individuals) or by immersion (195 individuals), and genotyped for 9654 markers using RAD-sequencing. Fifteen QTL associated with resistance traits were detected and only three QTL were common between the injection and immersion. Using a model that accounted for epistatic interactions between QTL, two main types of interactions were revealed. A "compensation-like" effect was detected between several pairs of QTL for the two modes of infection. An "enhancing-like" interaction effect was detected between four pairs of QTL. Integration of the QTL results with results of a previous transcriptomic analysis of response to F. psychrophilum infection resulted in a list of potential candidate immune genes that belong to four relevant functional categories (bacterial sensors, effectors of antibacterial immunity, inflammatory factors and interferon-stimulated genes). CONCLUSIONS: These results provide new insights into the genetic determinism of rainbow trout resistance to F. psychrophilum and confirm that some QTL with large effects are involved in this trait. For the first time, the role of epistatic interactions between resistance-associated QTL was evidenced. We found that the infection protocol used had an effect on the modulation of defence mechanisms and also identified relevant immune functional candidate genes

In memoriam - La Truite commune, Salmo trutta L.

International audienceCe Salmonidé est un poisson de pêche récréative extrêmement populaire. Son domaine de répartition initial (Europe, Haut Atlas, plateau anatolien et tributaires de la mer d'Aral) a été étendu, au début du xx.e siècle, à d'autres zones tempérées ou froides d'Amérique, d'Afrique et d'Asie par transplantation

Diversite genetique de la truite commune

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Gene segregation in gynogenetic brown trout (Salmo trutta L.) : systematically high frequencies of post-reduction

The post-reduction rates of 12 protein loci were measured in gynogenetic lines of brown trout obtained by retention of the second polar body. Post-reduction occurs frequently at all the loci (average rate = 0.88 ± 0.16) and is systematic at 7 of them. Similar results were previously observed in rainbow trout and complete interference could be a common feature in salmonids. The relationship between the degree of divergence of the duplicated loci and their recombination rate is also examined and discussed.Les taux de post-réduction de 12 locus enzymatiques ont été estimés dans des lignées gynogénétiques de truite fario obtenues par rétention du 2" globule polaire. La post-réduction se produit fréquemment à tous les locus (taux moyen = 0,88 ± 0,16) et systématiquement à 7 d’entre eux. Des résultats similaires ont déjà été obtenus chez la truite arc-en-ciel ; l’interférence totale pourrait donc être une caractéristique commune à tous les salmonidés. La relation entre le degré de divergence des locus dupliqués et leur taux de recombinaison est également examinée et discutée

Electrophoretic variation in six populations of brown trout (Salmo trutta L.).

Starch gel electrophoretic studies of 16 enzymes encoded by 34 Loci were performed on six brown trout populations. One new polymorphism is described at the Pmi-2 locus. Breeding data were analysed for both single and joint segregation of six loci: Aat-1, Cpk-1, G3p-2, Mdh-2, Mdh-3, and Pmi-2. All the loci are shown to segregate in simple mendelian ratios and one nonrandom joint segregation was observed. The polymorphism level, heterozygosities, and genetic distances were estimated and compared with those reported in other studies on brown trout and closely related salmonid species. The polymorphism level (25%) and average heterozygosity (9%) were high. Significant genetic distances were observed, but the average degree of differentiation between populations appeared to be small (9% of the total heterozygosity).L'électrophorèse sur gel d'amidon permet d'étudier chez six populations de truites brunes 16 enzymes associées à 34 loci. On fait état d'un nouveau polymorphisme au locus Pmi-2. Les données recueillies font l'objet d'une analyse, eu égard à la disjonction individuelle et groupée des six loci suivants : Aat-1, Cpk-1, G3p-2, Mdh-2, Mdh-3 et Pmi-2. Tous les loci se disjoignent conformément aux proportions mendéliennes classiques : une seule disjonction groupée et sélective est notée. Le degré de polymorphisme, le niveau d'hétérozygotie, ainsi que les distances génétiques, sont évalués et comparés aux valeurs rapportées dans d'autres études sur la truite brune et sur des espèces très apparentées. Les niveaux de polymorphisme (25%) et d'hétérozygotie (9%) sont élevés. Des distances génétiques significatives sont observées, mais le niveau moyen de différenciation entre les populations s'avère faible (9% de l'hétérozygotie totale)

A propos des périodes d'accélération de la croissance faciale

Cet article se propose d'analyser, à l'aide d'un atlas réalisé au Centre d'Étude de Croissance d'Ann Arbor (Michigan, U.S.A.) certains aspects de la croissance faciale. Les informations chiffrées figurant sur l'atlas ont été transposées sur des graphiques, qui ne reproduisent que les taux d'agrandissement moyen annuel des deux échantillons étudiés (36 filles et 47 garçons). Ces deux groupes ont été examinés de 6 à 16 ans, à raison d'une fois par an, au moment de leur anniversaire. L'étude des graphiques fait apparaître des notions différentes de celles transmises par l'École Danoise de BJØRK : les moments d'accélération de la croissance faciale ne sont pas limités à la période du pic pré-pubertaire ; ils apparaissent, sur l'échantillon étudié, avant et après ce stade, qui est présenté par BJØRK, comme synchrone de l'accélération de la croissance staturale. Par exemple, le taux d'augmentation de la croissance mandibulaire, chez les garçons, est particulièrement important, de 15 à 16 ans. Cette observation peut être prise en compte à propos du traitement de certaines anomalies

Les truites des rivières de Haute-Savoie sont-elles autochtones, sont -elles sauvages ?

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