Abstract

BackgroundOne 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).ResultsThe 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.ConclusionThese 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.

Highlights

  • One of the most important goals for the rainbow trout aquaculture industry is to improve fillet yield and fillet quality

  • Phenotypes and heritability estimates The total numbers of phenotyped fish for fillet yield and shear force were 775 and 772, respectively, and varied per year-class (YC) with 471 fish in YC 2012, and 304 fish in YC 2010

  • A slightly higher fillet yield and shear force were observed for fish from the YC 2012 compared to that from YC 2010

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Summary

Introduction

One of the most important goals for the rainbow trout aquaculture industry is to improve fillet yield and fillet quality. 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. 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). One of the challenges is the lack of genetically improved strains of fish for aquaculture [3, 4]. Selective breeding programs can produce fish of improved genetics for heritable traits that positively impact aquaculture production [5, 6].

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