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Original Research ARTICLE Provisionally accepted The full-text will be published soon. Notify me

Front. Genet. | doi: 10.3389/fgene.2019.00386

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

  • 1Middle Tennessee State University, United States
  • 2University of Alabama at Birmingham, United States
  • 3University of Georgia, United States
  • 4Cool and Cold Water Aquaculture Research (USDA-ARS), United States
  • 5West Virginia University, United States
  • 6Biology, Middle Tennessee State University, United States

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.

Keywords: rainbow trout, Fillet quality traits, Fillet firmness, softness, Shear force, protein content, GWAS, WssGBLUP, QTL

Received: 11 Feb 2019; Accepted: 10 Apr 2019.

Edited by:

Peng Xu, Xiamen University, China

Reviewed by:

Zhe Zhang, South China Agricultural University, China
JUN H. XIA, Sun Yat-sen University, China  

Copyright: © 2019 Ali, Al-Tobasei, Lourenco, Leeds, Kenney and Salem. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Prof. Mohamed Salem, Middle Tennessee State University, Biology, Murfreesboro, 37132, TN, United States,