Background Selective breeding is a relatively recent practice in aquaculture species compared to terrestrial livestock. Nevertheless, the genetic variability of farmed salmonid lines, which have been selected for several generations, should be assessed. Indeed, a significant decrease in genetic variability due to high selection intensity could have occurred, potentially jeopardizing the long-term genetic progress as well as the adaptive capacities of populations facing change(s) in the environment. Thus, it is important to evaluate the impact of selection practices on genetic diversity to limit future inbreeding. The current study presents an analysis of genetic diversity within and between six French rainbow trout ( Oncorhynchus mykiss ) experimental or commercial lines based on a medium-density single nucleotide polymorphism (SNP) chip and various molecular genetic indicators: fixation index ( F ST ), linkage disequilibrium (LD), effective population size ( N e ) and inbreeding coefficient derived from runs of homozygosity (ROH). Results Our results showed a moderate level of genetic differentiation between selected lines ( F ST ranging from 0.08 to 0.15). LD declined rapidly over the first 100 kb, but then remained quite high at long distances, leading to low estimates of N e in the last generation ranging from 24 to 68 depending on the line and methodology considered. These results were consistent with inbreeding estimates that varied from 10.0% in an unselected experimental line to 19.5% in a commercial line, and which are clearly higher than corresponding estimates in ruminants or pigs. In addition, strong variations in LD and inbreeding were observed along the genome that may be due to differences in local rates of recombination or due to key genes that tended to have fixed favorable alleles for domestication or production. Conclusions This is the first report on ROH for any aquaculture species. Inbreeding appeared to be moderate to high in the six French rainbow trout lines, due to founder effects at the start of the breeding programs, but also likely to sweepstakes reproductive success in addition to selection for the selected lines. Efficient management of inbreeding is a major goal in breeding programs to ensure that populations can adapt to future breeding objectives and SNP information can be used to manage the rate at which inbreeding builds up in the fish genome. Electronic supplementary material The online version of this article (10.1186/s12711-019-0468-4) contains supplementary material, which is available to authorized users.

Fillet yield (i.e. the proportion of edible flesh from a given amount of fish) is a trait of high economic interest for species sold as fillets. Improving it by selective breeding is not an easy task, as it is a ratio trait, which causes mathematical difficulties. It is moreover a specific ratio where numerator (fillet weight) and denominator (body weight) are very strongly correlated (genetic and phenotypic correlations in the range 0.89-0.99). This led some authors to conclude that they have the same genetic and phenotypic basis, precluding selection for improved fillet yield. In this study, we propose to study fillet yield as a component of two traits, fillet weight and waste weight (waste weight = body weight-fillet weight, so the sum of head, bones, fins and viscera weight), which we expect to be less correlated. Using data from 5 batches of fish from 3 species (sea bass, sea bream, rainbow trout), we show that as expected, fillet weight and waste weight are less correlated than fillet weight and body weight (on average, rA = 0.91 and rP = 0.88 vs. rA = 0.987, rP = 0.981). We used stochastic simulation to generate genotypes and phenotypes of fish using those genetic parameters for fillet weight and waste weight. We simulated 10 generations of selection for increased fillet yield using nine selection indices. Five indices had rather similar performances, residual fillet weight (the residual of the regression of fillet weight to body weight), fillet yield, fillet to waste ratio, restricted selection index (a linear index aimed at improving fillet weight while keeping waste weight constant) and linear index (optimized to improve fillet/waste ratio). With these indices, the average selection gain was + 0.66% of fillet yield per generation (range 0.30 to 0.95% using real genetic parameters from 5 fish batches). Selection for the difference between fillet weight and waste weight was 30% less efficient, while selection for increased fillet weight or increased body weight was 55-65% less efficient. Selection against waste weight had a null or even negative impact on fillet yield. Factors favorable to higher selection gains are low initial fillet yield, different heritabilities and CVs of fillet weight and waste weight, low genetic correlation and high phenotypic correlation of fillet weight and waste weight. These results suggest that although fillet weight and body weight are strongly correlated and proportional to each other, moderate selection gains on fillet yield are possible. We consider it would be useful to add waste weight in the parameters recorded in future genetic studies on fillet yield. Highlights ► We estimated genetic parameters of fillet weight and waste weight in fish. ► We performed stochastic simulations to evaluate gains in fillet yield. ► Fillet yield can be improved by 0.66% per generation on average in simulations. ► Fillet yield, fillet/waste ratio and fillet weight to body weight residuals are good selection indices. ► Selection for fillet weight or body weight performed poorly to improve f...