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Auteur Guinand, B.; Chauvel, C.; Lechene, M.; Tournois, J.; Tsigenopoulos, C.S.; Darnaude, A.M.; McKenzie, D.J.; Gagnaire, P.A.
Titre Candidate gene variation in gilthead sea bream reveals complex spatiotemporal selection patterns between marine and lagoon habitats Type Article scientifique
Année 2016 Publication Revue Abrégée Marine Ecology Progress Series
Volume (down) 558 Numéro Pages 115-127
Mots-Clés Amplicon sequencing; Candidate gene; Genetic differentiation; Growth hormone; Local selection; Prolactin
Résumé In marine fishes, the extent to which spatial patterns induced by selection remain stable across generations remains largely unknown. In the gilthead sea bream Sparus aurata, polymorphisms in the growth hormone (GH) and prolactin (Prl) genes can display high levels of differentiation between marine and lagoon habitats. These genotype-environment associations have been attributed to differential selection following larval settlement, but it remains unclear whether selective mortality during later juvenile stages further shapes genetic differences among habitats. We addressed this question by analysing differentiation patterns at GH and Prl markers together with a set of 21 putatively neutral microsatellite loci. We compared genetic variation of spring juveniles that had just settled in 3 ecologically different lagoons against older juveniles sampled from the same sites in autumn, at the onset of winter outmigration. In spring, genetic differentiation among lagoons was greater than expected from neutrality for both candidate gene markers. Surprisingly, this signal disappeared completely in the older juveniles, with no significant differentiation for either locus a few months later in autumn. We searched for signals of haplotype structure within GH and Prl genes using next-generation amplicon deep sequencing. Both genes contained 2 groups of haplotypes, but high similarities among groups indicated that signatures of selection, if any, had largely been erased by recombination. Our results are consistent with the view that differential selection operates during early juvenile life in sea bream and highlight the importance of temporal replication in studies of post-settlement selection in marine fish.
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ISSN 0171-8630, 1616-1599 ISBN Médium
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Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2239
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Auteur Vandeputte, M.; Fraslin, C.; Haffray, P.; Bestin, A.; Allal, F.; Kocour, M.; Prchal, M.; Dupont-Nivet, M.
Titre How to genetically increase fillet yield in fish: Relevant genetic parameters and methods to predict genetic gain Type Article scientifique
Année 2020 Publication Revue Abrégée Aquaculture
Volume (down) 519 Numéro Pages 734877
Mots-Clés Aquaculture; Genetics; Heritability; Linear index; Processing yields; Residual fillet weight; Selection; Selection response; Simulation
Résumé Fillet yield (i.e. the proportion of edible muscle in a fish) is a key economic trait for species sold as fillets. Its genetic improvement is complicated by several of its characteristics 1) it is a ratio trait, 2) its numerator (fillet weight) and denominator (body weight) are strongly correlated (correlations in the range 0.89–0.99), 3) it offers little phenotypic variation and 4) it cannot be measured on alive breeding candidates. In a former study, we showed that it could be improved by selection, especially with three selection indices, fillet yield, residual fillet weight and a ratio-specific linear index. However, it is well known that the heritability of ratio traits does not permit a reliable prediction of genetic gains. As predictability of genetic gains is a key requirement to define breeding programs, we investigated how genetic gains in fillet yield could be predicted by the genetic parameters of fillet yield, of residual fillet weight and of the component traits of the linear index. To this end, we compared simulated genetic gains with those estimated by classical prediction methods. This was done using real sets of genetic parameters obtained in nine populations of rainbow trout, European sea bass, gilthead sea bream and common carp. We show that the genetic parameters of fillet yield cannot be used to reliably predict genetic gains in fillet yield. Conversely, selection index theory using a linear index, combining either fillet weight and body weight or fillet weight and waste weight, provides almost perfect prediction of gains. Still, it is highly sensitive to the precision of the genetic and phenotypic correlations estimates, which should not be rounded to less than three decimals for fillet weight and body weight, while two decimals are appropriate for fillet weight and waste weight. A simple, reasonably precise alternative to the linear index is the use of residual fillet weight (the residual of the regression of fillet weight on body weight) as a surrogate for fillet yield.
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ISSN 0044-8486 ISBN Médium
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Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2722
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Auteur Haffray, P.; Enez, F.; Bugeon, J.; Chapuis, H.; Dupont-Nivet, M.; Chatain, B.; Vandeputte, M.
Titre Accuracy of BLUP breeding values in a factorial mating design with mixed families and marker-based parentage assignment in rainbow trout Oncorhynchus mykiss Type Article scientifique
Année 2018 Publication Revue Abrégée Aquaculture
Volume (down) 490 Numéro Pages 350-354
Mots-Clés Aquaculture; DNA parentage assignment; EBV accuracy; Salmonids; Sib selection
Résumé 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 microsatellite markers. The accuracy of EBVs was estimated using or removing individual performance to mimic combined family selection (with individual phenotype) or sib selection (without individual phenotype). The traits investigated had medium to high heritability (0.17–0.58). High to very high accuracy (0.630–0.817) was estimated for combined family selection. The accuracy of sib selection (not using individual phenotype) was 18–22% lower (0.542–0.638), but remained in the upper range reported for such traits. This level of accuracy was higher than those reported in conventional breeding programs using separate family rearing. This was true even for families with a very low number of full-sibs. Individual EBV accuracy was more closely linked to the total number of full- and half-sibs of each fish than to its number of full-sibs. We hypothesize that this was due to the factorial mating, which led to a high number of the genetic ties between sibs. These results highlight the possibility of introducing precise estimated breeding values for quality traits into combined or sib selection in breeding programs when using mixed families from factorial designs and marker-based parentage assignment in aquaculture species.
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Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2318
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Auteur Hillen, J.E.J.; Coscia, I.; Vandeputte, M.; Herten, K.; Hellemans, B.; Maroso, F.; Vergnet, A.; Allal, F.; Maes, G.E.; Volckaert, F.A.M.
Titre Estimates of genetic variability and inbreeding in experimentally selected populations of European sea bass Type Article scientifique
Année 2017 Publication Revue Abrégée Aquaculture
Volume (down) 479 Numéro Pages 742-749
Mots-Clés Artificial selection; ddRAD; fish; genetic diversity; Genomics; Inbreeding
Résumé 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 selected for growth over three generations and the second line for both high and low weight loss under a starvation regime over two generations. We used a genomic approach (2549 single nucleotide polymorphism markers derived from double digest restriction site associated DNA sequencing) in combination with eight microsatellites to estimate genetic variation, relatedness, effective population size and genetic differentiation across generations. Individual heterozygosity estimates indicated that the selected lines showed no significant reduction in diversity compared with wild populations. There was, however, a decreasing trend in allelic richness, suggesting the loss of low frequency alleles. We compared the estimates of effective population size from genetic markers with pedigree information and found good correspondence between methods. This study provides important insights in the genetic consequences of selective breeding and demonstrates the operational use of the latest genomic tools to estimate variability, inbreeding and at a later stage domestication and artificial selection.
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Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2183
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Auteur Vandeputte, M.; Puledda, A.; Tyran, A.S.; Bestin, A.; Coulombet, C.; Bajek, A.; Baldit, G.; Vergnet, A.; Allal, F.; Bugeon, J.; Haffray, P.
Titre Investigation of morphological predictors of fillet and carcass yield in European sea bass (Dicentrarchus labrax) for application in selective breeding Type Article scientifique
Année 2017 Publication Revue Abrégée Aquaculture
Volume (down) 470 Numéro Pages 40-49
Mots-Clés Genetics; Heritability; Indirect selection; Processing yields; Ultrasound tomography
Résumé 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 prediction was rather low for fillet yield (r2 = 0.02–0.18), but higher for carcass yield (r2 = 0.27–0.41). However, genetic correlations of predictors with the traits to predict were reasonably high (up to 0.67 for fillet yield and 0.95 for carcass yield), thus allowing to consider them for performing indirect individual selection instead of sib selection. However, it was difficult to design a predictor that would simultaneously increase fillet yield and carcass yield because of contradicting effects of relative head size, an important component of the predictors which was positively correlated to carcass yield but not to fillet yield.

Statement of relevance

We estimated phenotypic predictors for processing yields in the European sea bass and estimated their genetic variation and correlations with the traits to predict. This is important to be able to apply indirect selection for processing yields in this species. This showed that although the traits of interest were hardly correlated, it was not possible to find external predictors having a significant positive impacts on both traits (carcass and fillet yield) simultaneously. This highlights the need to study specifically these issues in different species and conditions, as the picture here is very different to the well studied case of rainbow trout for example.
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Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 1719
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