Fillet yield (FY, %), the ratio between the separable muscle of the fish and the harvest weight, is an economically important trait in rainbow trout aquaculture that reflects production efficiency with a consequent large impact on the returns (Kause et al., 2002). On a per-unit basis, the fillet price is three times that of the whole fish (Bugeon et al., 2010) and a recent global survey ranked FY among the six most important traits for genetic improvement in rainbow trout aquaculture (Sae-Lim et al., 2012). Despite that, FY has not received much attention in breeding programs because it is a lethally-measured trait, costly to measure, and difficult to select on, thus limiting the genetic progress in traditional selective breeding programs (Kause et al., 2007).