Background We used stable isotope profiling ( 15 N and 13 C) to obtain indicator phenotypes for feed efficiency in aquaculture. Our objectives were to (1) examine whether atom percent of stable isotopes of nitrogen and carbon can explain more of the variation in feed conversion ratio than growth alone, and (2) estimate the heritabilities of and genetic correlations between feed efficiency, growth and indicator traits as functions of nitrogen and carbon metabolism in various tissues. A 12-day experiment was conducted with 2281 Atlantic salmon parr, with an average initial weight of 21.8 g, from 23 full-sib families that were allocated to 46 family tanks and fed an experimental diet enriched with 15 N and 13 C. Results Using leave-one-out cross-validation, as much as 79% of the between-tank variation in feed conversion ratio was explained by growth, indicator traits, and sampling day, compared to 62% that was explained by growth and sampling day alone. The ratio of tissue metabolism, estimated by a change in isotope fractions relative to body growth, was used as an individual indicator for feed efficiency. For these indicator ratio traits, the estimated genetic correlation to feed conversion ratio approached unity but their heritabilities were low (0.06 to 0.11). These results indicate that feed-efficient fish are characterized by allocating a high fraction of their metabolism to growth. Among the isotope indicator traits, carbon metabolism in the liver had the closest estimated genetic correlation with feed conversion ratio on a tank level (− 0.9) but a low estimated genetic correlation with individually recorded feed efficiency indicator ratio traits. The underlying determinants of these correlations are largely unknown. Conclusions Our findings show that the use of indicator ratio traits to assess individual feed efficiency in Atlantic salmon has great prospects in selection programs. Given that large quantities of feeds with contrasting isotope profiles of carbon and/or nitrogen can be produced cost-effectively, the use of stable isotopes to monitor nitrogen and carbon metabolism in various tissues has potential for large-scale recording of individual feed efficiency traits, without requiring individual feed intake to be recorded.

The gut microbiome plays a key role in animal health and metabolism through the intricate functional interconnection between the feed, gut microbes, and the host. Unfortunately, in aquaculture, the links between gut microbes and fish genetics and production phenotypes are not well understood.In this study, we investigate the associations between gut microbial communities, fish feed conversion, and fish genetics in the domestic Atlantic salmon. Microbial community composition was determined for 230 juvenile fish from 23 full-sib families and was then regressed on growth, carbon and nitrogen metabolism, and feed efficiency. We only found weak associations between host genetics and microbial composition. However, we did identify significant (p < 0.05) associations between the abundance of three microbial operational taxonomical units (OTUs) and fish metabolism phenotypes. Two OTUs were associated with both carbon metabolism in adipose tissue and feed efficiency, while a third OTU was associated with weight gain.In conclusion, this study demonstrates an intriguing association between host lipid metabolism and the gut microbiota composition in Atlantic salmon.

In growing animals, individual variation in feed efficiency may arise from individual differences in growth rate and protein metabolism. Over a period of time, these factors will affect the ratio between ‘new’ vs. ‘old’ protein, which can be quantified using isotope profiling. The aim of this study was to investigate the relationship between relative weight gain and atom percentage excess 15N in the muscle, liver and mid‐intestine. A 50‐day experiment was conducted with a total of 375 fish initially fed a standard diet, subsequently replaced by one out of five experimental diets, enriched with 15N. In general, fast‐growing fish are expected to have a better feed efficiency, and the results show that this is captured by isotope profiling in liver and muscle tissues. Furthermore, individual variation in isotope content, that is relative fraction of ‘new’ protein, among fish with comparable growth rates was observed, most expressed around ~50% isotope saturation, indicating differences in protein degradation and replacement not attributed to growth. The results suggest that isotope profiles can be used as individual indicator traits for feed efficiency and that inclusion levels of stable isotopes of 1%–2% gave the most reliable results.

Background One objective of this study was to identify putative quantitative trait loci (QTL) that affect indicator phenotypes for growth, nitrogen, and carbon metabolism in muscle, liver, and adipose tissue, and for feed efficiency. Another objective was to perform an RNAseq analysis (184 fish from all families), to identify genes that are associated with carbon and nitrogen metabolism in the liver. The material consisted of a family experiment that was performed in freshwater and included 2281 individuals from 23 full-sib families. During the 12-day feed conversion test, families were randomly allocated to family tanks (50 fish per tank and 2 tanks per family) and fed a fishmeal-based diet labeled with the stable isotopes 15N and 13C at inclusion levels of 2 and 1%, respectively. Results Using a linear mixed-model algorithm, a QTL for pre-smolt growth was identified on chromosome 9 and a QTL for carbon metabolism in the liver was identified on chromosome 12 that was closely related to feed conversion ratio on a tank level. For the indicators of feed efficiency traits that were derived from the stable isotope ratios (15N and 13C) of muscle tissue and growth, no convincing QTL was detected, which suggests that these traits are polygenic. The transcriptomic analysis showed that high carbon and nitrogen metabolism was associated with individuals that convert protein from the feed more efficiently, primarily due to higher expression of the proteasome, lipid, and carbon metabolic pathways in liver. In addition, we identified seven transcription factors that were associated with carbon and nitrogen metabolism and located in the identified QTL regions. Conclusions Analyses revealed one QTL associated with pre-smolt growth and one QTL for carbon metabolism in the liver. Both of these traits are associated with feed efficiency. However, more accurate mapping of the putative QTL will require a more diverse family material. In this experiment, fish that have a high carbon and nitrogen metabolism in the liver converted protein from the feed more efficiently, potentially because of a higher expression of the proteasome, lipid, and carbon metabolic pathways in liver. Within the QTL regions, we detected seven transcription factors that were associated with carbon and nitrogen metabolism.

11The gut microbiome plays a key role in animal health and metabolism through the intricate 12 functional interconnection between the feed, gut microbes, and the host. Unfortunately, in 13 aquaculture, the links between gut microbes and fish genetics and production phenotypes are not 14 well understood. 15In this study, we investigate the associations between gut microbial communities, fish feed 16 conversion, and fish genetics in the domestic Atlantic salmon. Microbial community composition 17 was determined for 230 juvenile fish from 23 full-sib families and was then regressed on growth, 18 carbon and nitrogen metabolism, and feed efficiency. We only found weak associations between 19 host genetics and microbial composition. However, we did identify significant (p < 0.05) 20 associations between the abundance of three microbial operational taxonomical units (OTUs) and 21 fish metabolism phenotypes. Two OTUs were associated with both carbon metabolism in adipose 22 tissue and feed efficiency, while a third OTU was associated with weight gain. 23In conclusion, this study demonstrates an intriguing association between host lipid metabolism and 24 the gut microbiota composition in Atlantic salmon. 25 26