Genome-wide estimates of genetic diversity, inbreeding and effective size of experimental and commercial rainbow trout lines undergoing selective breeding

Selective breedingis a relatively recent practice in aquaculture species compared to terrestrial livestock. Nevertheless, the genetic variabilityof farmed salmonid lines, which have been selected for several generations, should be assessed. Indeed, a significant decrease in genetic variabilitydue to high selection intensity could have occurred, potentially jeopardizing the long-term genetic progress as well as the adaptive capacitiesof 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(FST), linkage disequilibrium (LD), effective population size(Ne) and inbreedingcoefficient derived from runsof homozygosity(ROH). Our results showed a moderate level of genetic differentiation between selected lines (FST 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 Ne in the last generation ranging from 24 to 68 depending on the line and methodology considered. These results were consistent with inbreedingestimates 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 inbreedingwere 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. This is the first report on ROH for any aquaculture species. Inbreedingappeared to be moderate to high in the six French rainbow trout lines, due to founder effectsat the start of the breeding programs, but also likely to sweepstakes reproductive success in addition to selection for the selected lines. Efficient management of inbreedingis a major goal in breeding programsto ensure that populations can adapt to future breeding objectives and SNP information can be used to manage the rate at which inbreedingbuilds up in the fish genome.