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ARS Home » Northeast Area » Leetown, West Virginia » Cool and Cold Water Aquaculture Research » Research » Publications at this Location » Publication #383510
Research Project: Integrated Research Approaches for Improving Production Efficiency in Salmonids

Location: Cool and Cold Water Aquaculture Research

Title: Genome-wide scan for common variants associated with intramuscular fat and moisture content in rainbow trout

Author
item ALI, ALI - University Of Maryland
item AL-TOBASEI, RAFET - Middle Tennessee State University
item LOURENCO, DANIELA - University Of Georgia
item Leeds, Timothy - Tim
item KENNEY, BRETT - West Virginia University
item SALEM, MOHAMED - University Of Maryland

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/20/2020
Publication Date: 7/31/2020
Citation: Ali, A., Al-Tobasei, R., Lourenco, D., Leeds, T.D., Kenney, B., Salem, M. 2020. Genome-wide scan for common variants associated with intramuscular fat and moisture content in rainbow trout. Biomed Central (BMC) Genomics. 21(529):1-17. https://doi.org/10.1186/s12864-020-06932-0.
DOI: https://doi.org/10.1186/s12864-020-06932-0

Interpretive Summary: Variation in fat and moisture content can affect the eating quality of rainbow trout fillets. Studies have shown that variation in these traits is heritable, which suggests that selective breeding can be used to optimize fat and moisture content and improve fillet quality. However, little is known about the genetic architecture of these traits. To increase our understanding, approximately 800 rainbow trout with fillet quality data were genotyped using a recently-developed single nucleotide polymorphism (SNP) chip that contains 50,000 transcribed genes to identify genes and gene pathways that are responsible for controlling fat and moisture content. This study identified more than 100 SNPs that were associated with fat and moisture content, and the genes containing these SNPs are primarily involved in lipid metabolism, cytoskeleton remodeling, and protein turnover. This work furthers our efforts to develop precision breeding approaches to improve important traits in rainbow trout populations by identifying SNPs that can be prioritized for genomic selection.

Technical Abstract: Background: Genetic improvement of fillet quality attributes is a priority of the aquaculture industry. Muscle composition impacts quality attributes such as flavor, appearance, texture, and juiciness. Fat and moisture make up about ~ 80% of the tissue weight. The genetic architecture underlying the fat and moisture content of the muscle is still to be fully explored in fish. A 50 K gene transcribed SNP chip was used for genotyping 789 fish with available phenotypic data for fat and moisture content. Genotyped fish were obtained from two consecutive generations produced in the National Center for Cool and Cold Water Aquaculture (NCCCWA) growth-selective breeding program. Estimates of SNP effects from weighted single-step GBLUP (WssGBLUP) were used to perform genome- wide association (GWA) analysis to identify quantitative trait loci (QTL) associated with the studied traits. Results: Using genomic sliding windows of 50 adjacent SNPs, 137 and 178 SNPs were identified as associated with fat and moisture content, respectively. Chromosomes 19 and 29 harbored the highest number of SNPs explaining at least 2% of the genetic variation in fat and moisture content. A total of 61 common SNPs on chromosomes 19 and 29 affected the aforementioned traits; this association suggests common mechanisms underlying intramuscular fat and moisture content. Additionally, based on single-marker GWA analyses, 8 and 24 SNPs were identified in association with fat and moisture content, respectively. Conclusion: SNP-harboring genes were primarily involved in lipid metabolism, cytoskeleton remodeling, and protein turnover. This work provides putative SNP markers that could be prioritized and used for genomic selection in breeding programs.