Abstract
Filet quality traits determine consumer satisfaction and affect profitability of the aquaculture industry. Soft flesh is a criterion for fish filet downgrades, resulting in loss of value. Filet firmness is influenced by many factors, including rate of protein turnover. A 50K transcribed gene SNP chip was used to genotype 789 rainbow trout, from two consecutive generations, produced in the USDA/NCCCWA selective breeding program. Weighted single-step GBLUP (WssGBLUP) was used to perform genome-wide association (GWA) analyses to identify quantitative trait loci affecting filet firmness and protein content. Applying genomic sliding windows of 50 adjacent SNPs, 212 and 225 SNPs were associated with genetic variation in filet shear force and protein content, respectively. Four common SNPs in the ryanodine receptor 3 gene (RYR3) affected the aforementioned filet traits; this association suggests common mechanisms underlying filet shear force and protein content. Genes harboring SNPs were mostly involved in calcium homeostasis, proteolytic activities, transcriptional regulation, chromatin remodeling, and apoptotic processes. RYR3 harbored the highest number of SNPs (n = 32) affecting genetic variation in shear force (2.29%) and protein content (4.97%). Additionally, based on single-marker analysis, a SNP in RYR3 ranked at the top of all SNPs associated with variation in shear force. Our data suggest a role for RYR3 in muscle firmness that may be considered for genomic- and marker-assisted selection in breeding programs of rainbow trout.
Highlights
Aquaculture continues to experience rapid growth worldwide
The fish population used for the current genome-wide association (GWA) analysis had average shear force of 475.7 ± 83.47 (g/g) and crude protein% = 20.64 ± 0.62
Our results suggest that calcium homeostasis, more likely through ryanodine receptor 3 gene (RYR3), and transcriptional/chromatin regulators have major roles in regulating genetic variability in muscle protein content
Summary
Aquaculture continues to experience rapid growth worldwide. for a sustainable industry, there is a need to produce fish filets with consistent quality and high value. Rainbow Trout Muscle Firmness GWAS (Destefanis et al, 2008) These factors include prerigor muscle processing, production and storage temperature, chilling protocols, genotype, handling stress, collagen content, extent of proteolysis, and the proximate composition of muscle (Castañeda et al, 2005; Bahuaud et al, 2010; Grzes et al, 2017). The increased level of stress has been reported as a major cause of gaping and filet softness (Jacobsen et al, 2017). Despite a well-developed understanding of meat tenderization that has been studied for decades in mammals, the need exists for genetic markers of the fish “gaping” and filet softness phenotypes (Ouali et al, 2013)
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