Combining Individual Phenotypes of Feed Intake with Genomic Data to Improve Feed Efficiency in Sea Bass

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.

在养殖场中测定鱼类的个体采食量极具挑战性，这使得直接针对饲料转化率（Feed Conversion Ratio, FCR）开展选育工作难以实现。本研究通过限制饲喂下的单养模式，对588尾海鲈的个体FCR进行了估算。同时，我们还测定了这些试验鱼禁食后的体重损失量与肌肉脂肪含量，将其作为FCR的潜在间接指示性状。该588尾试验鱼来自亲本群体的完全双列杂交，亲本群体分别针对禁食后体重损失量进行了双向选育：高损失组（F+）与低损失组（F-）。试验群体的系谱信息可追溯至曾祖代。我们对其中400尾子代及其祖先进行了1110个单核苷酸多态性（Single Nucleotide Polymorphism, SNPs）的基因分型，由此可估算各性状的基因组遗传力。水族箱养殖下的个体FCR与生长率均具有可遗传特性（基因组遗传力h²分别为0.47与0.76），且二者呈极强的遗传负相关（相关系数为-0.98），这表明在限制饲喂条件下，生长速度更快的鱼类饲料利用效率更高。水族箱养殖下的FCR表现为：携带两个F-亲本的个体FCR为1.38，表现最优；携带两个F+亲本的个体FCR为1.51，表现最差；而杂交个体（F+/F-或F-/F+）的FCR为1.46，处于中间水平。肌肉脂肪含量与水族箱养殖下的生长率及禁食期生长率均呈正遗传相关。由此可见，提升水族箱养殖下的生长速率、降低禁食后的体重损失量以及提高肌肉脂肪含量，均为可改善水族箱养殖条件下FCR的目标性状。改良上述性状同样可提升常规群体养殖条件下鱼类的FCR表现：本研究证实，由个体FCR表现优良的鱼类组成的养殖群体，其群体饲料利用效率显著更高。当养殖群体内个体的禁食期生长率估计育种值（Estimated Breeding Value, EBV）平均水平更高（即体重损失量更低）时，该群体的FCR表现也更优。因此，水族箱养殖下的FCR与禁食后体重损失量均为改良群体养殖条件下鱼类FCR的有效性状。最后，本研究证实，相较于基于系谱的最佳线性无偏预测（Best Linear Unbiased Prediction, BLUP），单步基因组最佳线性无偏预测（single-step genomic BLUP）下的估计育种值可靠性提升了10%至125%。这表明，当仅能通过水族箱养殖下的个体FCR表型测定获取有限数量的同胞个体信息时，基因组数据可有效提升候选选育个体的EBV预测准确性。