AbstractBackgroundThere are both economic and environmental motivations to improve feed efficiency. However, direct genetic improvement of feed efficiency ratio (FER; weight gain/feed intake) is difficult. Alternatively, improved FER might be achieved indirectly by selection for increased growth rate and reduced body fat. The aims of this study were (i) to perform a phenotypic analysis of energy partitioning traits among Atlantic salmon families; (ii) to estimate heritability and genetic relationships among feed efficiency and underlying traits; (iii) to determine an optimal breeding strategy to improve feed efficiency in Atlantic salmon.ResultsModerate genomic heritability estimates were obtained for most traits, e.g. feed intake (0.35), weight gain (0.42), feed efficiency ratio (0.19) and energy density of the gained weight (0.26). Heritability for residual feed intake was 0.04. Genetic correlation between feed efficiency and growth or energy density of the gained weight was 0.68 and -0.64, respectively. A selection index including weight gain and energy density of the gained weight was most beneficial to increase FER. The effect of body energy (reflecting fat deposition) was half of what could be predicted if energy efficiency (EE; energy gain/energy intake) was constant. The fish retained 50 and 49% of the energy and protein intake, respectively. Energy loss was due to heat (29% of intake), faecal loss (18%) and nitrogen excretion (3%). The derived energy and protein budget traits displayed low to moderate genomic heritability (h2 = 0.01–0.31). Protein efficiency reflected FER.ConclusionsGenetic selection for weight gain and against energy density of the gained weight will improve feed efficiency ratio in Atlantic salmon without the need for individual feed intake records. The results suggest that by selection against body energy, and given the same weight gain, 50% of the reduction in body energy can be realised as reduced feed intake and thus improved FER.