Quantitative trait loci for a neurocranium deformity, lack of opercullum, in gilthead seabream (Sparus aurata L.)

Lack of operculum, a neurocranial deformity, is the most common external abnormality to be found among industrially produced gilthead seabream (Sparus aurata L.), and this entails significant financial losses. This study conducts, for the first time in this species, a quantitative trait loci (QTL) analysis of the lack of operculum. A total of 142 individuals from a paternal half-sibling family (six full-sibling families) were selected for QTL mapping. They had previously shown a highly significant association with the prevalence of lack of operculum in a segregation analysis. All the fish were genotyped for 106 microsatellite markers using a set of multiplex PCRs (ReMsa1–ReMsa13). A linear regression methodology was used for the QTL analysis. Four QTL were detected for this deformity, two of which (QTLOP1 and QTLOP2) were significant. They were located at LG (linkage group) nine and LG10 respectively. Both QTL showed a large effect (about 27%), and furthermore, the association between lack of operculum and sire allelic segregation observed was statistically significant in the QTLOP1 analysis. These results represent a significant step towards including marker-assisted selection for this deformity in genetic breeding programmes to reduce the incidence of the deformity in the species

Comparing carbonate and organic AMS- (super 14) C ages in Lake Abiyata sediments (Ethiopia); hydrochemistry and paleoenvironmental implications.

Le Laboratoire de Géologie de la Matière Organique est intégré dans l'Institut des Sciences de la Terre d'Orléans - ISTO - CNRS Université d'OrléansWe studied a 12.6-m-long sequence from Lake Abiyata (Central Ethiopia) to establish a reliable and accurate chronology for use in global paleoclimatic reconstructions. The 26 accelerator mass spectrometry radiocarbon (AMS 14C) ages, performed on carbonates and organic matter, define 2 parallel chronologies, representing the complete Holocene period. However, these chronologies show a significant discrepancy from 500 to 900 BP in depth; ages obtained on carbonates were always older than those on organic matter. The hydrogeological and geochemical behavior of the Lake Abiyata basin has shed light on this discrepancy. We found that the carbonate crystallization is due mainly to the mixing of lake waters with groundwaters from the multi-layered aquifer contained in the 600-m-thick basement of the lake. The 14C activity of total dissolved inorganic carbon (TDIC) measured by AMS from bottom and surface lake waters (111.4 and 111.8 pMC, respectively) confirms that the mixing occurs at the water-sediment interface. This evidence of groundwater participation in the carbonate crystallization calls into question the current paleoclimatic reconstructions based on inorganic carbonates in lakes. Specific attention should thus be given to the respective proportions of each end-member in the mixing for the quantitative estimation of the groundwater input. This will help to validate the paleoenvironmental reconstructions and to highlight an eventual diagenetical evolution of inorganic carbonates during burial, via the study of pore waters

Genomic Prediction of Resistance to Pasteurellosis in Gilthead Sea Bream (Sparus aurata) Using 2b-RAD Sequencing

Gilthead sea bream (Sparus aurata) is a species of paramount importance to the Mediterranean aquaculture industry, with an annual production exceeding 140,000 metric tons. Pasteurellosis due to the Gram-negative bacterium Photobacterium damselae subsp. piscicida (Phdp) causes significant mortality, especially during larval and juvenile stages, and poses a serious threat to bream production. Selective breeding for improved resistance to pasteurellosis is a promising avenue for disease control, and the use of genetic markers to predict breeding values can improve the accuracy of selection, and allow accurate calculation of estimated breeding values of nonchallenged animals. In the current study, a population of 825 sea bream juveniles, originating from a factorial cross between 67 broodfish (32 sires, 35 dams), were challenged by 30 min immersion with 1 x 10(5) CFU virulent Phdp. Mortalities and survivors were recorded and sampled for genotyping by sequencing. The restriction-site associated DNA sequencing approach, 2b-RAD, was used to generate genome-wide single nucleotide polymorphism (SNP) genotypes for all samples. A high-density linkage map containing 12,085 SNPs grouped into 24 linkage groups (consistent with the karyotype) was constructed. The heritability of surviving days (censored data) was 0.22 (95% highest density interval: 0.11-0.36) and 0.28 (95% highest density interval: 0.17-0.4) using the pedigree and the genomic relationship matrix respectively. A genome-wide association study did not reveal individual SNPs significantly associated with resistance at a genome-wide significance level. Genomic prediction approaches were tested to investigate the potential of the SNPs obtained by 2b-RAD for estimating breeding values for resistance. The accuracy of the genomic prediction models (r = 0.38-0.46) outperformed the traditional BLUP approach based on pedigree records (r = 0.30). Overall results suggest that major quantitative trait loci affecting resistance to pasteurellosis were not present in this population, but highlight the effectiveness of 2b-RAD genotyping by sequencing for genomic selection in a mass spawning fish species

Coding Gene SNP Mapping Reveals QTL Linked to Growth and Stress Response in Brook Charr (Salvelinus fontinalis)

Growth performance and reduced stress response are traits of major interest in fish production. Growth and stress-related quantitative trait loci (QTL) have been already identified in several salmonid species, but little effort has been devoted to charrs (genus Salvelinus). Moreover, most QTL studies to date focused on one or very few traits, and little investigation has been devoted to QTL identification for gene expression. Here, our objective was to identify QTL for 27 phenotypes related to growth and stress responses in brook charr (Salvelinus fontinalis), which is one of the most economically important freshwater aquaculture species in Canada. Phenotypes included 12 growth parameters, six blood and plasma variables, three hepatic variables, and one plasma hormone level as well as the relative expression measurements of five genes of interest linked to growth regulation. QTL analysis relied on a linkage map recently built from S. fontinalis consisting of both single-nucleotide polymorphism (SNP, n = 266) and microsatellite (n =81) markers in an F2 interstrain hybrid population (n = 171). We identified 63 growth-related QTL and four stress-related QTL across 18 of the 40 linkage groups of the brook charr linkage map. Percent variance explained, confidence interval, and allelic QTL effects also were investigated to provide insight into the genetic architecture of growth- and stress-related QTL. QTL related to growth performance and stress response that were identified could be classified into two groups: (1) a group composed of the numerous, small-effect QTL associated with some traits related to growth (i.e., weight) that may be under the control of a large number of genes or pleiotropic genes, and (2) a group of less numerous QTL associated with growth (i.e., gene expression) and with stress-related QTL that display a larger effect, suggesting that these QTL are under the control of a limited number of genes of major effect. This study represents a first step toward the identification of genes potentially linked to phenotypic variation of growth and stress response in brook charr. The ultimate goal is to provide new tools for developing Molecular Assisted Selection for this species

Heritability of cortisol response to confinement stress in European sea bass dicentrarchus labrax

Background: In fish, the most studied production traits in terms of heritability are body weight or growth, stress or disease resistance, while heritability of cortisol levels, widely used as a measure of response to stress, is less studied. In this study, we have estimated heritabilities of two growth traits (body weight and length) and of cortisol response to confinement stress in the European sea bass. Findings: The F1 progeny analysed (n = 922) belonged to a small effective breeding population with contributions from an unbalanced family structure of just 10 males and 2 females. Heritability values ranged from 0.54 (+/- 0.21) for body weight to 0.65 (+/- 0.22) for standard body length and were low for cortisol response i.e. 0.08 (+/- 0.06). Genetic correlations were positive (0.94) between standard body length and body weight and negative between cortisol and body weight and between cortisol and standard body length (-0.60 and -0.55, respectively). Conclusion: This study confirms that in European sea bass, heritability of growth-related traits is high and that selection on such traits has potential. However, heritability of cortisol response to stress is low in European sea bass and since it is known to vary greatly among species, further studies are necessary to understand the reasons for these differences

Quantitative Trait Loci Involved in Sex Determination and Body Growth in the Gilthead Sea Bream (Sparus aurata L.) through Targeted Genome Scan

Among vertebrates, teleost fish exhibit a considerably wide range of sex determination patterns that may be influenced by extrinsic parameters. However even for model fish species like the zebrafish Danio rerio the precise mechanisms involved in primary sex determination have not been studied extensively. The zebrafish, a gonochoristic species, is lacking discernible sex chromosomes and the sex of juvenile fish is difficult to determine. Sequential protandrous hermaphrodite species provide distinct determination of the gender and allow studying the sex determination process by looking at the mechanism of sex reversal. This is the first attempt to understand the genetic basis of phenotypic variation for sex determination and body weight in a sequential protandrous hermaphrodite species, the gilthead sea bream (Sparus aurata). This work demonstrates a fast and efficient strategy for Quantitative Trait Loci (QTL) detection in the gilthead sea bream, a non-model but target hermaphrodite fish species. Therefore a comparative mapping approach was performed to query syntenies against two other Perciformes, the European sea bass (Dicentrarchus labrax), a gonochoristic species and the Asian sea bass (Lates calcarifer) a protandrous hermaphrodite. In this manner two significant QTLs, one QTL affecting both body weight and sex and one QTL affecting sex, were detected on the same linkage group. The co-segregation of the two QTLs provides a genomic base to the observed genetic correlation between these two traits in sea bream as well as in other teleosts. The identification of QTLs linked to sex reversal and growth, will contribute significantly to a better understanding of the complex nature of sex determination in S. aurata where most individuals reverse to the female sex at the age of two years through development and maturation of the ovarian portion of the gonad and regression of the testicular area. [Genomic sequences reported in this manuscript have been submitted to GenBank under accession numbers HQ021443–HQ021749.

Pleistocene eruptive chronology of the Gölcük volcano, Isparta Angle, Turkey. Chronologie des épisodes volcaniques pléistocènes du volcan Gölcük, Angle d’Isparta, Turquie

In the Eastern Mediterranean region, the Isparta volcanic belongs to the post-collisional alkali-potassic to ultrapotassic magmatism active since the Miocene in this part of the Anatolian peninsula from Afyon to Isparta. In the so-called Isparta Angle (IA) the magmatism is contemporaneous with an extensional regime intiated during Late Miocene and active throughout the Pliocene and Quaternary. Previous K/Ar dating performed on lavas suggested that potassic-ultrapotassic magmatism occurred between 4.7 to 4 Ma. However, a more recent (Quaternary) activity of the Gölcük volcano is evidenced by the present-day morphology and field evidence although it remained undated and poorly studied so far. Field mapping and new radiometric data indicate that the main volcano-forming stages of the Gölcük volcano consist of three main eruptives cycles. (1) Cycle I, represented by more than 200m-thick pyroclastic flow deposits occasionally separated by paleosoils and corresponding to caldera-forming ignimbritic eruptions. (2) Cycle II, consisting of tephriphonolite lava dome-flows extruded throughout the caldera and currently found along the rim of the present crater. (3) Cycle III made up of tuff-ring deposits related to several phreatoplinian eruptions of a maar-type volcanic activity. This youngest cycle ends with trachytic domes protruding within the maar crater. Unspiked 40K/40Ar dating on mesostasis was performed on lavas (tephriphonolites and trachytic domes), and complemented by preliminary 40Ar/39Ar data on tephra deposits (sanidine). Our preliminary results show that the entire activity of Gölcük volcano took place during the Pleistocene and was disconnected from the older Pliocene volcanism. This volcanic activity can be considered as a new volcanic cycle, starting (Cycle I) around 200 ka with major explosive, regional-scale, events represented by at least six ignimbrites sheets. Cycle II occurred between 115 ± 3 ka to 62 ± 2 ka with probably some associated tephra deposits. Tuff-ring of Cycle III formed from 72.7 ± 4.7 ka to 24 ± 2 ka. The associated phreatoplinian eruptions have almost entirely destroyed the previously formed flow-dome. This latest activity corresponds to several volcanic crises as illustrated by the two domes protrusions separated by about 30 ka. The volcanic history of Gölcük ceased around 24 ka ± 2 ka, but the periodicity of eruptive events appears to be long and complex. Currently, the volcano is at rest, but there is no doubt that the Isparta town (more than 120 000 people) built on top of the most recent tephra falls is exposed to a major volcanic hazard in the future.En Méditerranée Orientale, la région active d’Isparta est le siège d’un magmatisme alcalin lié à la distension affectant cette partie de la Péninsule Anatolienne depuis le Miocène supérieur. Le volcanisme Pliocène est alcalin et très potassique, depuis des magmas lamprophyriques à lamproïtiques, jusqu’à des téphriphonolites et des trachytes. La construction du volcan Gölcük au sud d’Isparta marque le début d’un nouveau cycle éruptif après une longue période d’arrêt et d’érosion. L’étude morpho-structurale du volcan couplée aux datations 40K/40Ar sur lave et 39Ar/40Ar sur monograin de feldspath-K indique une histoire éruptive complexe, nettement plus jeune que l’activité antérieure (Pliocène). Ces résultats préliminaires montrent que l’activité volcanique du Gölcük est située dans le Pléistocène supérieur (Paléolithique) entre environ 200 ka et 24 ka. Trois cycles volcaniques majeurs sont reconnus : (1) Cycle I débutant vers 200 ka avec des éruptions ignimbritiques majeures avec un ensemble de coulées pyroclastiques trachytiques comblant les paléo-vallées ouvertes dans les formations sédimentaires et les formations volcaniques d’âge pliocène ; (2) Cycle II avec un épisode effusif de faible importance succède entre 115 ± 3 ka et 62 ± 2 ka à l’activité explosive initiale avec la mise en place d’un édifice central constitué de dômes-coulées téphri-phonolitiques ; (3) Cycle III entre 70 ka et 24 ka, l’activité devient phréatoplinienne et suit de près le cycle précédent. Le dynamisme éruptif phréatomagmatique est celui d’un maar formé d’un large cratère d’explosion entouré d’un anneau de tufs. La dernière crise volcanique se termine par l’extrusion de plusieurs dômes de trachyte dans le cratère et de téphras associés, de nouvelles coulées pyroclastiques se mettent vraisemblablement en place vers le nord-ouest. Les données de terrain et les âges 40Ar/39Ar disponibles indiquent que ces dernières manifestations (construction du maar) sont très récentes et sub-contemporaines du dernier niveau de retombées ponceuses sous les immeubles de la ville et des dômes de lave intra-caldeira. Cet âge récent est confirmé par un âge 14C obtenu sur des bois carbonisés. La morphologie du volcan actuel est relativement bien conservée, malgré l’érosion très active qui remodèle déjà partiellement les pentes. La reprise éventuelle de l’activité du volcan constituerait un risque majeur à l’échelle de la région et en particulier pour la ville d’Isparta établie au pied de l’édifice, notamment sur les coulées pyroclastiques et les retombées ponceuses les plus récentes