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A medium-throughput method to phenotype fish for individual feed efficiency ArchiMer
Besson, Mathieu; Allal, Francois; Chatain, Beatrice; Vergnet, Alain; Clota, Frederic; Ferrari, Sebastien; Vandeputte, Marc.
Tipo: Text
Ano: 2017 URL: http://archimer.ifremer.fr/doc/00446/55752/57413.pdf
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Combining Individual Phenotypes of Feed Intake With Genomic Data to Improve Feed Efficiency in Sea Bass ArchiMer
Besson, Mathieu; Allal, Francois; Chatain, Beatrice; Vergnet, Alain; Clota, Frederic; Vandeputte, Marc.
Measuring individual feed intake of fish in farms is complex and precludes selective breeding for feed conversion ratio (FCR). Here, we estimated the individual FCR of 588 sea bass using individual rearing under restricted feeding. These fish were also phenotyped for their weight loss at fasting and muscle fat content that were possibly linked to FCR. The 588 fish were derived from a full factorial mating between parental lines divergently selected for high (F+) or low (F–) weight loss at fasting. The pedigree was known back to the great grand-parents. A subset of 400 offspring and their ancestors were genotyped for 1,110 SNPs which allowed to calculate the genomic heritability of traits. Individual FCR and growth rate in aquarium were both heritable...
Tipo: Text Palavras-chave: Aquaculture; Feed conversion ratio; Fine phenotyping; Genomic selection; Individual feed intake; Restricted feeding; Selective breeding.
Ano: 2019 URL: https://archimer.ifremer.fr/doc/00486/59799/62927.pdf
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Combining vitassign and colony: an efficient practical procedure for parental assignment with missing parents ArchiMer
Doan, Q.k.; Vandeputte, Marc; Chatain, Beatrice; Vergnet, Alain; Allal, Francois.
Tipo: Text
Ano: 2015 URL: http://archimer.ifremer.fr/doc/00281/39196/37750.pdf
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Combining vitassign and colony for pedigree reconstruction in a case of factorial mating with missing parental genotypes ArchiMer
Allal, Francois; Doan, Q.k.; Chatain, Beatrice; Vergnet, Alain; Vandeputte, Marc.
Tipo: Text
Ano: 2015 URL: http://archimer.ifremer.fr/doc/00306/41694/40971.pdf
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Combining Vitassign and Colony for pedigree reconstruction in a case of factorial mating with missing parental genotypes ArchiMer
Allal, Francois; Doan, Q.k.; Chatain, Beatrice; Vergnet, Alain; Vandeputte, Marc.
Tipo: Text
Ano: 2015 URL: http://archimer.ifremer.fr/doc/00281/39180/37742.pdf
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Contribution of a bioenergetics model to investigate the growth and survival of European seabass in the Bay of Biscay – English Channel area ArchiMer
Dambrine, Chloe; Huret, Martin; Woillez, Mathieu; Pecquerie, Laure; Allal, Francois; Servili, Arianna; De Pontual, Helene.
The European seabass (Dicentrarchus labrax) is a species of particular ecological and economic importance. Stock assessments have recently revealed the worrying state of the “Northern stock”, probably due to overfishing and a series of poor recruitments. The extent to which these poor recruitments are due to environmental variability is difficult to assess, as the processes driving the seabass life cycle are poorly known. Here we investigate how food availability and temperature may affect the growth and survival of wild seabass at the individual scale. To this end, we developed a bioenergetics model based on the Dynamic Energy Budget (DEB) theory. We applied it to seabass population of the Northeast Atlantic region (Bay of Biscay – English Channel area)...
Tipo: Text Palavras-chave: Dicentrarchus labrax Northeast Atlantic Dynamic Energy Budget theory Growth; Starvation Early-life stages.
Ano: 2020 URL: https://archimer.ifremer.fr/doc/00612/72397/71341.pdf
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Dynamic epimarks in sex-related genes predict gonad phenotype in the European sea bass, a fish with mixed genetic and environmental sex determination ArchiMer
Anastasiadi, Dafni; Vandeputte, Marc; Sanchez-baizan, Nuria; Allal, Francois; Piferrer, Francesc.
The integration of genomic and environmental influences into methylation patterns to bring about a phenotype is of central interest in developmental epigenetics, but many details are still unclear. The sex ratios of the species used here, the European sea bass, are determined by genetic and temperature influences. We created four families from parents known to produce offspring with different sex ratios, exposed larvae to masculinizing temperatures and examined, in juvenile gonads, the DNA methylation of seven genes related to sexual development by a targeted sequencing approach. The genes most affected by both genetics and environment were cyp19a1a and dmrt1, with contrasting sex-specific methylation and temperature responses. The relationship between...
Tipo: Text Palavras-chave: Early development; Environmental temperature; DNA methylation; Sex determination; Aromatase; Cyp19a1a; Dmrt1; Epigenetic marks; DNA methylation threshold; Epigenetic inheritance.
Ano: 2018 URL: https://archimer.ifremer.fr/doc/00470/58123/61657.pdf
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Estimates of genetic variability and inbreeding in experimentally selected populations of European sea bass ArchiMer
Hillen, J. E. J.; Coscia, I.; Vandeputte, Marc; Herten, K.; Hellemans, B.; Maroso, F.; Vergnet, Alain; Allal, Francois; Maes, G. E.; Volckaert, F. A. M..
The aquaculture industry has increasingly aimed at improving economically important traits like growth, feed efficiency and resistance to infections. Artificial selection represents an important window of opportunity to significantly improve production. However, the pitfall is that selection will reduce genetic diversity and increase inbreeding in the farmed stocks. Genetic tools are very useful in this context as they provide accurate measures of genetic diversity together with many additional insights in the stock status and the selection process. In this study we assessed the level of genetic variability and relatedness over several generations of two lines of experimentally selected European sea bass (Dicentrarchus labrax L.). The first line was...
Tipo: Text Palavras-chave: Artificial selection; DdRAD; Fish; Genetic diversity; Genomics; Inbreeding.
Ano: 2017 URL: http://archimer.ifremer.fr/doc/00392/50314/50993.pdf
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Estimation of genetic parameters of feed conversion ratio based on individual phenotypes and genomic data in sea bass ArchiMer
Besson, Mathieu; Allal, Francois; Chatain, Beatrice; Vergnet, Alain; Clota, Frederic; Ferrari, Sebastien; Vandeputte, Marc.
We estimated genetic parameters of feed conversion ratio (FCR) and daily growth coefficient (DGC) using individual phenotypes measured in aquariums under a restricted feeding regime and genomic information on 2,722 SNP markers. The results showed a moderate heritability of both traits (0.26 for FCR and 0.41 for DGC) as well as close to unity negative genetic correlation between them. Thus, FCR of fish in aquariums could be improved by selecting fish for higher DGC. Nevertheless, these results must be taken with caution until we know whether individual FCR measured in aquariums also reflects the FCR of fish reared in groups.    
Tipo: Text Palavras-chave: Feed efficiency; Fish; Genomics.
Ano: 2018 URL: http://archimer.ifremer.fr/doc/00446/55756/57416.pdf
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First Evidence of Realized Selection Response on Fillet Yield in Rainbow Trout Oncorhynchus mykiss, Using Sib Selection or Based on Correlated Ultrasound Measurements ArchiMer
Vandeputte, Marc; Bugeon, Jérôme; Bestin, Anastasia; Desgranges, Alexandre; Allamellou, Jean-michel; Tyran, Anne-sophie; Allal, Francois; Dupont-nivet, Mathilde; Haffray, Pierrick.
Fillet yield, the proportion of edible fillet relative to body weight, is a major trait to improve in fish sold processed, as it has a direct impact on profitability and can simultaneously decrease the environmental impact of producing a given amount of fillet. However, it is difficult to improve by selective breeding, because it cannot be measured on live breeding candidates, its phenotypic variation is low, and, as a ratio, it is not normally distributed and a same change in fillet yield can be the result of different changes in fillet weight and body weight. Residual headless gutted carcass weight (rHGCW) is heritable and highly genetically correlated to Fillet% in rainbow trout, and can be predicted by the ratio of abdominal wall thickness to depth of...
Tipo: Text Palavras-chave: Aquaculture; Fillet yield; Selective breeding; Selection response; Production efficiency; Heritability.
Ano: 2019 URL: https://archimer.ifremer.fr/doc/00599/71121/69423.pdf
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Genetic variation of resistance to Viral Nervous Necrosis and genetic correlations with production traits in wild populations of the European sea bass ( Dicentrarchus labrax ) ArchiMer
Khanh, Doan Quoc; Vandeputte, Marc; Chatain, Beatrice; Haffray, Pierrick; Vergnet, Alain; Breuil, Gilles; Allal, Francois.
Viral Nervous Necrosis (VNN) disease is considered as one of the most serious threats for European sea bass cultured in Mediterranean Sea, with no simple and effective procedures to treat this disease. In this study, 1472 offspring resulting from artificial full factorial mating of western Mediterranean dams with sires from four different wild populations of European sea bass (Northern Atlantic, NAT; Western Mediterranean, WEM; Northern-East Mediterranean, NEM; and Southern-East Mediterranean, SEM) were challenged by experimental infection to W80 betanodavirus strain in order to evaluate genetic variations for VNN resistance among populations and genetic correlations between VNN resistance and production traits. The results showed a large variation of VNN...
Tipo: Text Palavras-chave: VNN disease; VNN resistance; Heritability; Genetic correlation.
Ano: 2017 URL: http://archimer.ifremer.fr/doc/00385/49612/50124.pdf
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Genome-wide association and genomic prediction of resistance to viral nervous necrosis in European sea bass (Dicentrarchus labrax) using RAD sequencing ArchiMer
Palaiokostas, Christos; Cariou, Sophie; Bestin, Anastasia; Bruant, Jean-sebastien; Haffray, Pierrick; Morin, Thierry; Cabon, Joelle; Allal, Francois; Vandeputte, Marc; Houston, Ross D..
Background: European sea bass (Dicentrarchus labrax) is one of the most important species for European aquaculture. Viral nervous necrosis (VNN), commonly caused by the redspotted grouper nervous necrosis virus (RGNNV), can result in high levels of morbidity and mortality, mainly during the larval and juvenile stages of cultured sea bass. In the absence of efficient therapeutic treatments, selective breeding for host resistance offers a promising strategy to control this disease. Our study aimed at investigating genetic resistance to VNN and genomic-based approaches to improve disease resistance by selective breeding. A population of 1538 sea bass juveniles from a factorial cross between 48 sires and 17 dams was challenged with RGNNV with mortalities and...
Tipo: Text
Ano: 2018 URL: https://archimer.ifremer.fr/doc/00445/55676/57357.pdf
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Heritability of Boldness and Hypoxia Avoidance in European Seabass, Dicentrarchus labrax ArchiMer
Ferrari, Sebastien; Horri, Khaled; Allal, Francois; Vergnet, Alain; Benhaim, David; Vandeputte, Marc; Chatain, Beatrice; Begout, Marie-laure.
To understand the genetic basis of coping style in European seabass, fish from a full factorial mating (10 females x 50 males) were reared in common garden and individually tagged. Individuals coping style was characterized through behavior tests at four different ages, categorizing fish into proactive or reactive: a hypoxia avoidance test (at 255 days post hatching, dph) and 3 risk-taking tests (at 276, 286 and 304 dph). We observed significant heritability of the coping style, higher for the average of risk-taking scores (h2 = 0.45 ± 0.14) than for the hypoxia avoidance test (h2 = 0.19 ± 0.10). The genetic correlations between the three risk-taking scores were very high (rA = 0.96–0.99) showing that although their repeatability was moderately high (rP =...
Tipo: Text
Ano: 2016 URL: https://archimer.ifremer.fr/doc/00362/47278/47239.pdf
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How could fully scaled carps appear in natural waters in Madagascar? ArchiMer
Hubert, Jean-noel; Allal, Francois; Hervet, Caroline; Ravakarivelo, Monique; Jeney, Zsigmond; Vergnet, Alain; Guyomard, Rene; Vandeputte, Marc.
The capacity of organisms to rapidly evolve in response to environmental changes is a key feature of evolution, and studying mutation compensation is a way to evaluate whether alternative routes of evolution are possible or not. Common carps (Cyprinus carpio) carrying a homozygous loss-of-function mutation for the scale cover gene fgfr1a1, causing the 'mirror' reduced scale cover, were introduced in Madagascar a century ago. Here we show that carps in Malagasy natural waters are now predominantly covered with scales, though they still all carry the homozygous mutation. We also reveal that the number of scales in mutated carps is under strong polygenic genetic control, with a heritability of 0.49. As a whole, our results suggest that carps submitted to...
Tipo: Text Palavras-chave: Evolution; Mutation compensation; Heritability.
Ano: 2016 URL: http://archimer.ifremer.fr/doc/00356/46681/46725.pdf
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Improving feed efficiency in fish using selective breeding: a review ArchiMer
De Verdal, Hugues; Komen, Hans; Quillet, Edwige; Chatain, Beatrice; Allal, Francois; Benzie, John A. H.; Vandeputte, Marc.
Improving feed efficiency (FE) is key to reducing production costs in aquaculture and to achieving sustainability for the aquaculture industry. Feed costs account for 30–70% of total production costs in aquaculture; much work has been done on nutritional and husbandry approaches to improve FE but only a limited amount of research has been devoted to using genetics, despite its potential. This paper reviews past work to improve FE in fish using selective breeding and assess future directions. Direct selection on FE traits requires methods to measure individual feed consumption and estimate FE efficiently and accurately. This is particularly difficult to do in fish because of the environment in which they live. Many of the published studies on FE were found...
Tipo: Text Palavras-chave: Feed conversion ratio; Feed efficiency; Feed intake; Fish; Genetics; Selection.
Ano: 2018 URL: https://archimer.ifremer.fr/doc/00415/52675/53771.pdf
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Investigation of morphological predictors of fillet and carcass yield in European sea bass (Dicentrarchus labrax) for application in selective breeding ArchiMer
Vandeputte, Marc; Puledda, Antonio; Tyran, Anne Sophie; Bestin, Anastasia; Coulombet, Celine; Bajek, Aline; Baldit, Gwenaelle; Vergnet, Alain; Allal, Francois; Bugeon, Jerome; Haffray, Pierrick.
Genetic parameters for carcass and fillet percentage were estimated in 760 European sea bass reared under commercial conditions and slaughtered at 573 days post fertilization (395 g mean body weight). Phenotyped fish were the offspring of 45 sires and 20 dams crossed in a factorial mating design. Pedigrees were re-constructed with 90.7% success using 12 microsatellites. The heritability of fillet yield was moderately low (0.21), while it was high for carcass yield (0.57). Both traits were poorly correlated (− 0.01 to 0.28) making space for their combined improvement. We investigated different predictors derived from measurement of surfaces on digital pictures and ultrasound measurements at several points of the body. The accuracy of the phenotypic...
Tipo: Text Palavras-chave: Ultrasound tomography; Genetics; Heritability; Indirect selection; Processing yields.
Ano: 2017 URL: http://archimer.ifremer.fr/doc/00361/47217/47173.pdf
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Population-specific variations of the genetic architecture of sex determination in wild European sea bass Dicentrarchus labrax L. ArchiMer
Faggion, Sara; Vandeputte, Marc; Chatain, Beatrice; Gagnaire, Pierre-alexandre; Allal, Francois.
Polygenic sex determination (PSD) may show variations in terms of genetic and environmental components between populations of fish species exposed/adapted to different environments. The European sea bass (Dicentrarchus labrax) is an interesting model, combining both a PSD system and a genetic subdivision into an Atlantic and a Mediterranean lineage, with genetic substructures within the Mediterranean Sea. Here, we produced experimental progeny crosses (N = 927) from broodstock sampled in four wild populations (North Atlantic, NAT; Western Mediterranean, WEM; North-Eastern Mediterranean, NEM; South-Eastern Mediterranean, SEM). We found less females than males in the progeny, both in the global dataset (32.5%) and within each paternal group (from 25.1% for...
Tipo: Text
Ano: 2019 URL: https://archimer.ifremer.fr/doc/00464/57609/59864.pdf
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The European sea bass: a key marine fish model in the wild and in aquaculture ArchiMer
Vandeputte, Marc; Gagnaire, P.‐a.; Allal, Francois.
The European sea bass (Dicentrarchus labrax L.) is a marine fish of key economic and cultural importance in Europe. It is now more an aquaculture than a fisheries species (>96% of the production in 2016), although modern rearing techniques date back only from the late 1980s. It also has high interest for evolutionary studies, as it is composed of two semispecies (Atlantic and Mediterranean lineages) that have come into secondary contact following the last glaciation. Based on quantitative genetics studies of most traits of interest over the past 10–15 years, selective breeding programs are now applied to this species, which is at the beginning of its domestication process. The availability of a good quality reference genome has accelerated the...
Tipo: Text Palavras-chave: Dicentrarchus labrax; Genetics; Heritability; Population genetics.
Ano: 2019 URL: https://archimer.ifremer.fr/doc/00486/59752/62858.pdf
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The origin and remolding of genomic islands of differentiation in the European sea bass ArchiMer
Duranton, Maud; Allal, Francois; Fraisse, Christelle; Bierne, Nicolas; Bonhomme, Francois; Gagnaire, Pierre-alexandre.
Speciation is a complex process that leads to the progressive establishment of reproductive isolation barriers between diverging populations. Genome-wide comparisons between closely related species have revealed the existence of heterogeneous divergence patterns, dominated by genomic islands of increased divergence supposed to contain reproductive isolation loci. However, this divergence landscape only provides a static picture of the dynamic process of speciation, during which confounding mechanisms unrelated to speciation can interfere. Here we use haplotype-resolved whole-genome sequences to identify the mechanisms responsible for the formation of genomic islands between Atlantic and Mediterranean sea bass lineages. Local ancestry patterns show that...
Tipo: Text
Ano: 2018 URL: https://archimer.ifremer.fr/doc/00446/55750/57409.pdf
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Viral encephalopathy and retinopathy in aquaculture: a review ArchiMer
Doan, Q. K.; Vandeputte, Marc; Chatain, Beatrice; Morin, T; Allal, Francois.
Viral encephalopathy and retinopathy (VER), otherwise known as viral nervous necrosis (VNN), is a major devastating threat for aquatic animals. Betanodaviruses have been isolated in at least 70 aquatic animal species in marine and in freshwater environments throughout the world, with the notable exception of South America. In this review, the main features of betanodavirus, including its diversity, its distribution and its transmission modes in fish, are firstly presented. Then, the existing diagnosis and detection methods, as well as the different control procedures of this disease, are reviewed. Finally, the potential of selective breeding, including both conventional and genomic selection, as an opportunity to obtain resistant commercial populations, is...
Tipo: Text Palavras-chave: Betanodavirus; Disease resistance; Genetics; Nervous necrosis virus; Selective breeding.
Ano: 2017 URL: https://archimer.ifremer.fr/doc/00350/46132/46024.pdf
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