Muscle/fillet is the most valuable product of fish. Increasing fillet yield and reducing fillet downgrading can improve production efficiency and customer satisfaction and have significant economic benefits.
fillet yield and requires several generations. The aquaculture industry is eager to adopt genomic selection methods to increase the efficiency of genetic improvement, i.e., increasing the accuracy of breeding values and reducing generation intervals, consequently increasing genetic gain.
In this project, we demonstrated the utility of genomic selection in fillet yield and quality traits of rainbow trout. We developed a 50K "functional" SNP chip and used it to identify QTL for fillet yield, firmness, color, protein, and fat contents. Our studies showed that the genomic predictions can improve the estimated breeding values by 33.3% for the fillet yield and 53.1% for fillet firmness.
The genomic predictions outperformed the traditional breeding by 35% for fillet yield and 42% for fillet firmness. In addition, we demonstrated that a reduced SNP panel of ~1000 SNPs used in genomic predictions still can provide predictive abilities higher than traditional breeding. These results suggest that genomic selection is a practical strategy to identify and select fish with superior genetic merit within rainbow trout families, even with low-density SNP panels.
Separately, a recent study in our laboratory indicated the presence of heritable fillet yield-associated microbiome components. We are currently assessing the feasibility of improving genetic prediction accuracy when microbiome information is integrated into genomics-metagenomics analyses.