Genome-wide association study identifies genomic loci affecting fillet firmness and protein content in rainbow trout

Authors: ALI, ALI - Middle Tennessee State University; AL-TOBASEI, RAFET - Middle Tennessee State University; LOURENCO, DANIELA - University Of Georgia; Leeds, Timothy - Tim; KENNEY, BRETT - West Virginia University; SALEM, MOHAMED - Middle Tennessee State University

Submitted to: Frontiers in Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/10/2019
Publication Date: 5/3/2019
Citation: Ali, A., Al-Tobasei, R., Lourenco, D., Leeds, T.D., Kenney, B., Salem, M. 2019. Genome-wide association study identifies genomic loci affecting fillet firmness and protein content in rainbow trout. Frontiers in Genetics. 10(386):1-17. https://doi.org/10.3389/fgene.2019.00386.
DOI: https://doi.org/10.3389/fgene.2019.00386

Interpretive Summary: Production of rainbow trout foodfish with fillets that have a consistent and high quality is critical for the growth and sustainability of the domestic aquaculture industry. Previous studies have identified factors that affect fillet quality and have demonstrated that these factors are heritable, and these studies collectively suggest that fillet quality can be improved using traditional selective breeding. However, fillet quality is a lethally-measured trait that cannot be directly measured on breeding candidates, and very little is known about the genes that affect variation in this trait. These factors have limited the efforts and progress toward improving fillet quality in salmonid populations via selective breeding. Scientists recently developed a high-density array (50,000 SNP chip) to genotype for polymorphisms that occur within exons, which are the DNA sequences within a gene that are transcribed into RNA and ultimately translated into proteins. This study used the recently-developed high-density array to genotype fish from a population that was characterized for fillet quality traits to conduct a genome-wide association analysis. This analysis identified hundreds of polymorphisms occurring within gene that associate with variation in fillet quality. This study furthers our understanding of the genetic architecture of fillet quality traits and identifies genes that may be targeted for genomic- and marker-assisted selective breeding approaches to improve fillet quality in rainbow trout populations.

Technical Abstract: Fillet quality traits determine consumer satisfaction and affect profitability of the aquaculture industry. Soft flesh is a criterion for fish fillet downgrades, resulting in loss of value. Fillet 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 fillet firmness and protein content. Applying genomic sliding windows of 50 adjacent SNPs, 212 and 225 SNPs were associated with genetic variation in fillet shear force and protein content, respectively. Four common SNPs in the ryanodine receptor 3 gene (RYR3) affected the aforementioned fillet traits; this association suggests common mechanisms underlying fillet 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.