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Besson, M., Allal, F., Chatain, B., Vergnet, A., Clota, F., & Vandeputte, M. (2019). Combining Individual Phenotypes of Feed Intake With Genomic Data to Improve Feed Efficiency in Sea Bass. Front. Genet., 10.
Résumé: Measuring individual feed intake of fish in farms is complex and precludes direct 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 as possible indirect indicators of FCR. The 588 fish were 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 grandparents. A subset of 400 offspring and their ancestors were genotyped for 1,110 SNPs, which allowed estimating the genomic heritability of traits. Individual FCR and growth rate in aquarium were both heritable (genomic h² = 0.47 and 0.76, respectively) and strongly genetically correlated (-0.98), meaning that under restricted feeding, faster growing fish were more efficient. FCR in aquariums was significantly better for fish with two F- parents (1.38), worse for fish with two F+ parents (1.51) and intermediate (1.46) for crossbred fish (F+/F- or F-/F+). Muscle fat content was positively genetically correlated to growth rate in aquarium and during fasting. Thus, higher growth rate in aquariums, lower weight loss at fasting and fat content are all traits that could improve FCR in aquarium. Improving these traits would also improve FCR of fish in normal group rearing conditions, as we showed that groups composed of fish with good individual FCR were significantly more efficient in groups. The FCR of groups was also better when the fish composing the groups had, on average, lower estimated breeding values for growth rate during fasting (losing less weight). Thus, FCR in aquarium and weight loss at fasting are both promising to improve FCR of fish in groups. Finally, we showed that the reliability of estimated breeding values was higher (from +10% to +125%) with single-step genomic BLUP than with pedigree-based BLUP, showing that genomic data would enhance the accuracy of EBV prediction o in selection candidates from a limited number of sibs individually phenotyped for FCR in aquariums.
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Doan, K. Q., Vandeputte, M., Chatain, B., Morin, T., & Allal, F. (2017). Viral encephalopathy and retinopathy in aquaculture: a review. J Fish Dis, 40(5), 717–742.
Résumé: 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 examined.
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Vandeputte, M., Bugeon, J., Bestin, A., Desgranges, A., Allamellou, J. - M., Tyran, A. - S., et al. (2019). First Evidence of Realized Selection Response on Fillet Yield in Rainbow Trout Oncorhynchus mykiss, Using Sib Selection or Based on Correlated Ultrasound Measurements. Front. Genet., 10, 1225.
Résumé: 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 the peritoneal cavity (E8/E23), measured on live fish by ultrasound tomography. We selected broodstock based on rHGCW, measured on sibs of the selection candidates, on ultrasound measurements (E8/E23) measured on the selection candidates, or a combination of both. Seven broodstock groups were selected: fish with 15% highest (rHGCW+) or lowest (rHGCW-) EBV for rHGCW, with 15% highest (E8/E23+) or lowest (E8/E23-) EBV for E8/E23, with both rHGCW+ and E8/E23+ (Both+) or rHGCW- and E8/E23- (Both-), or with close to zero EBVs for both traits (Mid). Seven corresponding groups of offspring were produced and reared communally. At harvest size (1.5 kg mean weight), 1,561 trout were slaughtered, measured for the traits of interest, and pedigreed with DNA fingerprinting. Offspring from groups Both+, rHGCW+ and E8/E23+ had a higher EBV for rHGCW than the control group, while down-selected groups had a lower EBV. Looking at the phenotypic mean for Fillet% (correlated response), up-selected fish had more fillet than down-selected fish. The highest difference was between Both+ (69.36%) and Both- (68.20%), a 1.16% units difference in fillet percentage. The change in Fillet% was explained by an opposite change in Viscera%, while Head% remained stable. Selection using sib information on rHGCW was on average more efficient than selection using the candidates' own E8/E23 phenotypes, and downward selection (decreasing Fillet%) was more efficient than upward selection.
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VANDEPUTTE, M., Porte, J. D., Auperin, B., Dupont-Nivet, M., VERGNET, A., Valotaire, C., et al. (2016). Quantitative genetic variation for post-stress cortisol and swimming performance in growth-selected and control populations of European sea bass (Dicentrarchus labrax). Aquaculture, 455, 1–7.
Résumé: Sea bass is a major species in Mediterranean aquaculture, and is now being subject to selective breeding programs for faster growth. In terrestrial species, it was demonstrated that fast growth may be linked to a correlated degradation of fitness traits. In this experiment, we evaluated 600 young sea bass from a factorial mating of 76 sires and 13 dams. The sires were from four genetic groups, wild (W), domesticated (D), and selected for growth (2 groups, M and P). The 600 offspring were submitted to two acute confinement stress challenges at 6 weeks intervals, and plasma cortisol at one hour post stress was measured. The same fish were also submitted to two swimming challenges at a 5 days interval, where the maximum sustained swimming speed (Umax) of each fish was evaluated. Parentage was assessed by genotyping of 12 microsatellites. 554 fish had both valid parentage and phenotypes. Cortisol had a low repeatability (r = 0.30 between the two successive measurements) while repeatability was moderate for Umax (r = 0.62). However, genetic correlations between successive measurements were very high (> 0.96) for both traits, indicating that successive measurements were related to the same trait. Heritability was moderate for mean post-stress cortisol (h2 = 0.34 ± 0.09) and Umax (h2 = 0.48 ± 0.08). When Umax was expressed in m.s− 1, it was negatively correlated to cortisol (rA = − 0.48 ± 0.08) and weakly correlated to body weight (rA = 0.12 ± 0.16), but figures changed when it was expressed in Body Lengths.s− 1(h2 = 0.55 ± 0.08, rA = − 0.10 ± 0.19 with cortisol and rA = − 0.64 ± 0.07 with body weight, respectively). Cortisol was moderately negatively correlated with body weight (rA = − 0.36 ± 0.18). The four lines did not differ for cortisol or Umax, but when Umax was expressed in BL.s− 1 it tended to be lower in the two selected lines – which were also significantly larger. However, this is likely due to a phenotypic decrease of relative Umax with increasing body size. We conclude that selection for growth and/or domestication should not impact maximum sustained swimming speed in the European sea bass, but may tend to favour animals with low cortisol responsiveness. These traits could be used to orientate functional capabilities other than productivity in sea bass.
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