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Accuracy of BLUP breeding values in a factorial mating design with mixed families and marker-based parentage assignment in rainbow trout Oncorhynchus mykiss ArchiMer
Haffray, Pierrick; Enez, Florian; Bugeon, Jerome; Chapuis, Herve; Dupont-nivet, Mathilde; Chatain, Beatrice; Vandeputte, Marc.
Marker-based parentage assignment provides the opportunity to investigate factors of efficiency for mixed-family designs and factorial mating. In such designs, family size is both uncontrolled and small, which may be thought to limit the accuracy of estimated breeding values (EBVs). The objective of this work was to estimate the accuracy of EBVs of growth and quality traits in a large factorial mating design and in commercial breeding conditions. An expected six hundred full-sib families of rainbow trout Oncorhynchus mykiss (2042 fish in total) were produced by ten factorial matings of six dams with ten sires. Fish were phenotyped for body weight, carcass yield, fillet yield, fillet fat content and fillet colour, and family information was recovered using...
Tipo: Text Palavras-chave: Aquaculture; Salmonids; DNA parentage assignment; Sib selection; EBV accuracy.
Ano: 2018 URL: https://archimer.ifremer.fr/doc/00429/54062/55395.pdf
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Body shape variation in meiotic gynogenetic and triploid sea bass, Dicentrarchus labrax ArchiMer
Peruzzi, Stefano; Wiborg-dahle, Stine; Haffray, Pierrick; Chatain, Beatrice; Primicerio, Raul.
A method of geometric morphometrics was used to characterize body shape variation in meiotic gynogenetic and triploid sea bass in comparison with diploid controls. A total of 13 coordinate landmark data were recorded on the profile of 34-month-old control (n = 81), gynogenetic (n = 117) and triploid (n = 131) siblings generated from two females (A and B). Three main axes of morphometric variation were consistent, and these accounted for 60.8 and 57.6% of the total variability in females A and B, respectively. There were significant shape deviations of triploid and gynogenetic fish relative to the controls, and differences were particularly evident in the progeny of one female. Overall, triploids displayed a more slender shape than diploids, whereas...
Tipo: Text Palavras-chave: Body shape variability; Morphometry; Geometry of Procrustes distance; Triploidy; Gynogenesis; European sea bass; Dicentrarchus labrax.
Ano: 2010 URL: http://archimer.ifremer.fr/doc/00025/13651/10757.pdf
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Compte rendu final du projet Triplofimer : Fiabilité et qualité de la production de naissains triploïdes d'huître creuse (Crassostrea gigas) ArchiMer
Suquet, Marc; Agogue, Julie; Brizard, Raphael; Haffray, Pierrick; Labbe, Catherine; Le Coz, Jean-rene; Pepin, Jean-francois; Rault, Paul; Saulnier, Denis.
Ce rapport fait état d'une étude réalisée au laboratoire de Génétique et Pathologie de l'IFREMER dans le cadre de l'analyse d'épisodes de mortalité anormale survenue en écloserie privée de crevettes pénéides. Plusieurs hypothèses ont été avancées. La présence de Vibrio harveyi a amené à constituer une collection de 40 souches à partir desquelles une identification bactériologique a été effectuée. Elle montre en effet une dominance de souches appartenant à un groupe homogène de Vibrio harveyi. La technique de ribotypage (digestion d'ADN génomique, transfert de Southem-blot et hybridation avec une sonde spécifique) est alors mise en place. Plusieurs difficultés techniques ont ralenti l'analyse et n'ont donc pas permis d'avoir des résultats assez avancés pour...
Tipo: Text Palavras-chave: Huître creuse; Crassostrea gigas; Tétraploïdes; Sperme; Conservation; Diagnostic zoo-sanitaire; Flore bactérienne; Herpès virus..
Ano: 2007 URL: http://archimer.ifremer.fr/doc/00304/41554/40762.pdf
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Conséquences génétiques de la production de larves d'huîtres en écloserie : étude des processus de dérive et de sélection ArchiMer
Taris, Nicolas; Sauvage, Christopher; Batista, Frederico; Baron, Sophie; Ernande, Bruno; Haffray, Pierrick; Boudry, Pierre.
Previous studies have shown heritable variation in larval developmental traits in the Pacific oyster Crassostrea gigas. In order to study the genetic consequences of production of oyster larvae in hatcheries, two factors, specific to hatcheries, were examined: the effect of discarding the smallest larvae (i.e. culling) and the effect of temperature (20°C versus 26°C). A mixed-family approach was used in order to infer the genetic composition of larval populations and family assignment, limiting possible environmental bias and allowing the study of a relatively large number of families using a limited number of larval tanks. Our results show that three multiplexed highly polymorphic microsatellite markers are a powerful tool for family assignment and,...
Tipo: Text Palavras-chave: Hatchery; Genetic diversity; Selection domestication; Larvae; Crassostrea gigas; Ecloserie; Diversité génétique; Sélection domestication; Larve; Crassostrea gigas.
Ano: 2006 URL: http://archimer.ifremer.fr/doc/2006/acte-1505.pdf
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CRYOAQUA. Centralisation de la cryoconservation et du stockage des ressources génétiques aquacoles françaises ArchiMer
Labbe, Catherine; Suquet, Marc; Michel, Gildas; Duclos, Delphine; Lemarchand, Alain; Le Hellec, Catherine; Vandeputte, Marc; Quittet, Benjamin; Goardon, Lionel; Pincent, Cedric; Haffray, Pierrick.
Tipo: Text
Ano: 2012 URL: http://archimer.ifremer.fr/doc/00099/20979/18602.pdf
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Cryopreservation of Pacific oyster ( Crassostrea gigas ) larvae: Revisiting the practical limitations and scaling up the procedure for application to hatchery ArchiMer
Labbe, Catherine; Haffray, Pierrick; Mingant, Christian; Quittet, Benjamin; Diss, Blandine; Tervit, H. Robin; Adams, Serean L.; Rimond, Flore; Suquet, Marc.
Pacific oyster Crassostrea gigas is one major species for aquaculture, and the development of breeding programs and the need for preservation of wild stock genetic resources prompted the need for larvae cryopreservation. The objective of the present study was to choose the most reliable protocol from several existing publications, to test its biological and practical limitations, and to adapt it to hatchery conditions. The selected protocol was characterized by a very slow freezing rate without seeding, and by the use of ethylene glycol and sucrose as cryoprotectant. The best survivals after thawing and rearing up to 48 h post fertilization (hpf) were obtained with larvae that were frozen at late trochophore (20 hpf) and early-D (24 hpf) stages. Increasing...
Tipo: Text Palavras-chave: Oyster; Cryobanking; D stage; Ethylene glycol; High throughput; Hatchery.
Ano: 2018 URL: https://archimer.ifremer.fr/doc/00423/53460/54354.pdf
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Estimates of heritability and genotype-environment interactions for body weight in sea bass (Dicentrarchus labrax L.) raised under communal rearing conditions ArchiMer
Saillant, Eric; Dupont Nivet, Mathilde; Haffray, Pierrick; Chatain, Beatrice.
Genetic parameters for somatic growth rate in sea bass were estimated in two experiments where 27 (year-class 1997) to 30 (year-class 1998) families of sea bass (3 dams mated with 9-10 sires according to a full factorial design) were raised mixed in the same tanks starting shortly before hatching (48 h post fertilization). Trials were performed under two temperature (experiment 1, 1997: group high temperature (HT) and group low temperature (LT)) and two density regimes (experiment 2, 1998: group high density (HD) and group low density (LD)) with a subset of the mating design (18 families) being reproduced in the two experiments. All the fish were genotyped at 3-6 microsatellite loci which allowed them to be assigned to the individual breeders used in the...
Tipo: Text Palavras-chave: Genotype x environment interaction; Communal rearing; Microsatellites markers; Dicentrarchus labrax; Growth; Heritability.
Ano: 2006 URL: http://archimer.ifremer.fr/doc/2006/publication-1706.pdf
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European sea bass - Dicentrarchus labrax ArchiMer
Haffray, Pierrick; Tsigenopoulos, C.s.; Bonhomme, Francois; Chatain, Beatrice; Magoulas, Antonio; Rye, M; Triantafyllidis, A; Triantafyllidis, C.
Tipo: Text
Ano: 2007 URL: http://archimer.ifremer.fr/doc/00134/24535/22567.pdf
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Flesh quality in large rainbow trout with high or low fillet yield ArchiMer
Bugeon, Jerome; Lefevre, Florence; Cardinal, Mireille; Uyanik, Ayhan; Davenel, Armel; Haffray, Pierrick.
Rainbow trout with different fillet yield [56 and 65% for low (LY) and high yield (HY), respectively] were examined for muscle organization and flesh quality (instrumental and sensorial evaluations). Both groups had similar body weight (3.6 kg in mean), but the HY group had a higher carcass yield (+15%). Higher total muscle area in the HY group (+20%) was associated with a higher number of muscle fibers (+22%). Flesh of the HY group presented a higher area of myosepta (+10%), fat content (+10%) and luminosity (+6%). Raw fillet mechanical resistance was higher for the HY group; an opposite result was obtained for cooked flesh. Sensorial evaluation of cooked flesh revealed no important differences between groups. Smoked fillet from the HY group presented...
Tipo: Text
Ano: 2010 URL: http://archimer.ifremer.fr/doc/00014/12532/9532.pdf
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Genetic improvement of fish: Achievements and challenges for tomorrow ArchiMer
Vandeputte, Marc; Baroiller, Jean-francois; Haffray, Pierrick; Quillet, Edwige.
Genetic improvement is a major contributing factor in developing efficient aquaculture, as it is in other forms of animal production. Moreover, as most fish species are only slightly domesticated, the potential gains are very large. Many of the current methods, developed during the XXth century, are classically used in livestock rearing (choice of breeds, crossbreeding, selective breeding). Others are much more specific to aquatic organisms (genetic control of sex, sterilization through triploidization). The spread of selected lines in aquaculture has been effective only since the 1990s, with lines selected essentially on growth and producing some impressive results. Transgenesis, although technically feasible on growth rate, is not used in practice and...
Tipo: Text Palavras-chave: Selection; Genomics; Fishes; Breeding; Aquaculture.
Ano: 2009 URL: http://archimer.ifremer.fr/doc/2009/publication-6564.pdf
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Genetic parameters of in-vivo prediction of carcass, head and fillet yields by internal ultrasound and 2D external imagery in large rainbow trout (Oncorhynchus mykiss) ArchiMer
Haffray, Pierrick; Bugeon, Jerome; Rivard, Quentin; Quittet, Benjamin; Puyo, Sophie; Allamelou, Jean Michel; Vandeputte, Marc; Dupont-nivet, Mathilde.
Selection to improve processing yields relies on sib selection, in which live candidates are ranked according to their family breeding value. This approach limits genetic progress, as it only exploits genetic variability between families and not within them. Indirect criteria measured on live candidates could overcome this limitation. The present study (1) proposes a procedure to identify indirect criteria to predict processing yields in rainbow trout (head, carcass and fillet yields), (2) estimates genetic parameters of these indirect criteria, and (3) predicts relative genetic gains in processing yields using full-sib selection or indirect individual selection on those indirect criteria. DNA-pedigreed all-female rainbow trout Oncorhynchus mykiss (n =...
Tipo: Text Palavras-chave: Salmonids; Heritability; Fillet yield; Selection; Aquaculture; Morphometry.
Ano: 2013 URL: http://archimer.ifremer.fr/doc/00157/26847/25249.pdf
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Genetic variability and selective breeding for traits of aquacultural interest in the Pacific oyster (Crassostrea gigas) ArchiMer
Boudry, Pierre; Degremont, Lionel; Taris, Nicolas; Mccombie, Helen; Haffray, Pierrick; Ernande, Bruno.
The most significant genetic improvement for production of Pacific oyster (Crassastrea gigas) has been obtained through the breeding of triploids, especially since the development of tetraploids. Quantitative genetics studies suggest that significant gains, for disease resistance or for other traits of aquacultural interest, could be obtained using this approach. However, the limited extent of hatchery-propagation (versus natural recruitment) and/or various technical difficulties and biological characteristics of the species have slowed the development of selective breeding programs. Recently, in the USA, Australia and New Zealand, family-based selective breeding programs have been initiated to improve growth and yield. In Europe, where both natural and...
Tipo: Text Palavras-chave: Microsatellites; Quantitative genetic; Genetic variability; Crassostrea gigas; Oysters.
Ano: 2004 URL: http://archimer.ifremer.fr/doc/2004/publication-2861.pdf
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Genetic variability and selective breeding for traits of aquacultural interest in the Pacific oyster (Crassostrea gigas) (slides) ArchiMer
Boudry, Pierre; Degremont, Lionel; Taris, Nicolas; Mccombie, Helen; Haffray, Pierrick; Ernande, Bruno.
To date, the most significant genetic improvement for the production of Pacific oyster (Crassostrea gigas) has been obtained through the breeding of triploids, especially since the development of tetraploids. Quantitative genetics studies suggest that significant gains, for disease resistance or for other traits of aquacultural interest, could be obtained in diploids using this approach. However, the limited extent of hatchery-propagation (versus natural recruitment) and/or various technical difficulties and biological characteristics of the species have retarded the development of selective breeding programs. Recently, in the U.S.A., Australia and New Zealand, countries where hatcheries are a major source of C. gigas juveniles, family-based selective...
Tipo: Text Palavras-chave: Microsatellite markers; Selective breeding; Genetic; Genetic variability; Crassostrea gigas; Pacific oysters.
Ano: 2004 URL: http://archimer.ifremer.fr/doc/2004/acte-3449.pdf
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Genetic variation for carcass quality traits in cultured sea bass (Dicentrarchus labrax) ArchiMer
Saillant, Eric; Dupont-nivet, Mathilde; Sabourault, Marie; Haffray, Pierrick; Laureau, Stanislas; Vidal, Marie-odile; Chatain, Beatrice.
Genetic parameters for carcass quality traits were estimated in 27 families of sea bass (3 dams x 9 sires factorial mating design), raised mixed in the same tanks starting before hatching. O. spring parentage was determined a posteriori using 6 microsatellite loci. Carcass quality traits were recorded at 818 days post fertilization (mean standard length: 32.6 +/- 3.1 cm). Genetic parameters were estimated from the sire half sib variance and covariance components. Heritability of body weight (BW) and carcass processing traits (standardized to body weight) percent head weight (Head%), percent viscera weight (Viscera%) and percent visceral fat weight (VisceFat%) were relatively high ranging from 0.48 +/- 0.15 (Viscera%) to 0.87 +/- 0.23 (Head%); the estimate...
Tipo: Text Palavras-chave: Dicentrarchus labrax; Communal testing; Microsatellites markers; Carcass quality; Heritability.
Ano: 2009 URL: http://archimer.ifremer.fr/doc/2009/publication-6355.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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Genotype by environment interactions for growth in European seabass (Dicentrarchus labrax) are large when growth rate rather than weight is considered ArchiMer
Dupont-nivet, Mathilde; Karahan-nomm, Bilge; Vergnet, Alain; Merdy, Olivier; Haffray, Pierrick; Chavanne, Herve; Chatain, Beatrice; Vandeputte, Marc.
Two hundred fifty three full-sib families from 33 males and 23 females of European seabass were produced in a partly factorial mating design. All fish were reared in the same tank for 14 months until reaching mean weight of 35 g. then 7000 of them were individually tagged and weighed, and dispatched to four farms in different locations (France, Israel, Italy and Portugal) representing a wide variety of environmental conditions. Around mean weight of 400 g. 1177 to 1667 fish at each site were weighed. Daily growth coefficient (DGC) was calculated. Pedigrees were successfully redrawn for 99.2% of fish using microsatellite markers. Genetic correlations between sites were high for body weight (>0.80 in all cases but one, i.e., five cases over six), but only...
Tipo: Text Palavras-chave: Dicentrarchus labrax; Seabass; Growth; Daily growth coefficient; Heritability; G x E interactions; Aquaculture.
Ano: 2010 URL: http://archimer.ifremer.fr/doc/00011/12256/9227.pdf
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How to genetically increase fillet yield in fish: New insights from simulations based on field data ArchiMer
Fraslin, Clemence; Dupont-nivet, Mathilde; Haffray, Pierrick; Bestin, Anastasia; Vandeputte, Marc.
Fillet yield (i.e. the proportion of edible flesh from a given amount of fish) is a trait of high economic interest for species sold as fillets. Improving it by selective breeding is not an easy task, as it is a ratio trait, which causes mathematical difficulties. It is moreover a specific ratio where numerator (fillet weight) and denominator (body weight) are very strongly correlated (genetic and phenotypic correlations in the range 0.89–0.99). This led some authors to conclude that they have the same genetic and phenotypic basis, precluding selection for improved fillet yield. In this study, we propose to study fillet yield as a component of two traits, fillet weight and waste weight (waste weight = body weight-fillet weight, so the sum of head, bones,...
Tipo: Text Palavras-chave: Aquaculture; Genetics; Heritability; Selection; Processing yields.
Ano: 2018 URL: https://archimer.ifremer.fr/doc/00415/52599/53430.pdf
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Improvement of chilled seabass sperm conservation using a cell culture medium ArchiMer
Fauvel, Christian; Boryshpolets, Sergey; Cosson, J.; Leedy, J. G. Wilson; Labbe, C.; Haffray, Pierrick; Suquet, Marc.
The sperm of seabass is very fragile and it quickly loses its ability to fertilize after collection either if kept undiluted or in classic saline media. In order to avoid cryopreservation when only short conservation is required, the process of sperm management including sperm collection, sperm dilution rate in storage medium and storage medium composition, was subject to experimental trials. A concentration of 20% urine generated a low pH of seminal fluid, and it immediately altered the motility ability. However, pH did not seem to be the key agent of motility prevention since sperm dilution in Leibovitz culture medium (L15) or in classic saline medium both presenting a similar low pH (7.3) did not affect motility. L15 increased the duration of sperm...
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Ano: 2012 URL: http://archimer.ifremer.fr/doc/00111/22221/20066.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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