Genomic predictions for fillet yield and firmness in rainbow trout using reduced-density SNP panels

• Published in: BMC genomics Vol. 22; no. 1; p. 92
• Main Authors: Al-Tobasei, Rafet, Ali, Ali, Garcia, Andre L S, Lourenco, Daniela, Leeds, Tim, Salem, Mohamed
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 30.01.2021; BioMed Central; BMC
• Subjects: Accuracy; Animals; Aquaculture; Breeding; Catfish; Density; Disease; EBV; Estimates; Fillets; Firmness; Fish; Fishes; GEBV; Gene mapping; Genetic aspects; Genomic selection; Genomics; Genotype; Identification and classification; LD pruning; Models, Genetic; Oncorhynchus mykiss; Oncorhynchus mykiss - genetics; Panels; Phenotype; Physiological aspects; Polymorphism, Single Nucleotide; Predictions; Predictive ability; Quantitative trait loci; Rainbow trout; Salmon; Single nucleotide polymorphisms; Single-nucleotide polymorphism; Trout; Yield; United States; EBV; LD pruning; GEBV; Genomic selection; Predictive ability
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/s12864-021-07404-9

One of the most important goals for the rainbow trout aquaculture industry is to improve fillet yield and fillet quality. Previously, we showed that a 50 K transcribed-SNP chip can be used to detect quantitative trait loci (QTL) associated with fillet yield and fillet firmness. In this study, data from 1568 fish genotyped for the 50 K transcribed-SNP chip and ~ 774 fish phenotyped for fillet yield and fillet firmness were used in a single-step genomic BLUP (ssGBLUP) model to compute the genomic estimated breeding values (GEBV). In addition, pedigree-based best linear unbiased prediction (PBLUP) was used to calculate traditional, family-based estimated breeding values (EBV). The genomic predictions outperformed the traditional EBV by 35% for fillet yield and 42% for fillet firmness. The predictive ability for fillet yield and fillet firmness was 0.19-0.20 with PBLUP, and 0.27 with ssGBLUP. Additionally, reducing SNP panel densities indicated that using 500-800 SNPs in genomic predictions still provides predictive abilities higher than PBLUP. These results suggest that genomic evaluation is a feasible strategy to identify and select fish with superior genetic merit within rainbow trout families, even with low-density SNP panels.