Relatedness determination in the absence of pedigree information in three cultured strains of rainbow trout ( Oncorhynchus mykiss)

Abstract

We evaluate the utility of a relatedness estimator ( r) as a tool for inbreeding avoidance in three aquaculture strains of rainbow trout ( Oncorhynchus mykiss) that show different amounts of genetic variation. The predicted distributions of r values for unrelated, half-sib and full-sib individuals based on population allele frequencies at 11–13 microsatellite loci were compared to those obtained from the genotypes of known parents. In two of the three strains, the r distributions derived from simulated progeny of known parents were significantly lower than those predicted using pairs of individuals created from strain-specific allele frequencies. This was most pronounced for the strain with the lowest average number of alleles per locus and derived from a very limited number of founders. The net result of these left shifts in the distributions is an underestimation of relatedness. In contrast, the third strain showed a more modest but significant right shift for the curves derived from the simulated progeny. The result of the right shift would be a reduction in the amount of related pairs assigned as unrelated for a given value of r. Thus, the probability of assigning related pairs as unrelated will increase markedly in aquaculture populations with histories of inbreeding and genetic bottlenecks.