Weighted Single-Step GWAS Identifies Genes Influencing Fillet Color in Rainbow Trout

Ridwan O Ahmed; Ali Ali; Rafet Al-Tobasei; Tim Leeds; Brett Kenney; Mohamed Salem

doi:10.3390/genes13081331

Weighted Single-Step GWAS Identifies Genes Influencing Fillet Color in Rainbow Trout

Genes (Basel). 2022 Jul 26;13(8):1331. doi: 10.3390/genes13081331.

Authors

Ridwan O Ahmed¹, Ali Ali¹, Rafet Al-Tobasei², Tim Leeds³, Brett Kenney⁴, Mohamed Salem¹

Affiliations

¹ Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA.
² Computational Science Program, Middle Tennessee State University, Murfreesboro, TN 37132, USA.
³ United States Department of Agriculture Kearneysville, National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, Kearneysville, WV 25430, USA.
⁴ Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV 26506, USA.

Abstract

The visual appearance of the fish fillet is a significant determinant of consumers' purchase decisions. Depending on the rainbow trout diet, a uniform bright white or reddish/pink fillet color is desirable. Factors affecting fillet color are complex, ranging from the ability of live fish to accumulate carotenoids in the muscle to preharvest environmental conditions, early postmortem muscle metabolism, and storage conditions. Identifying genetic markers of fillet color is a desirable goal but a challenging task for the aquaculture industry. This study used weighted, single-step GWAS to explore the genetic basis of fillet color variation in rainbow trout. We identified several SNP windows explaining up to 3.5%, 2.5%, and 1.6% of the additive genetic variance for fillet redness, yellowness, and whiteness, respectively. SNPs are located within genes implicated in carotenoid metabolism (β,β-carotene 15,15'-dioxygenase, retinol dehydrogenase) and myoglobin homeostasis (ATP synthase subunit β, mitochondrial (ATP5F1B)). These genes are involved in processes that influence muscle pigmentation and postmortem flesh coloration. Other identified genes are involved in the maintenance of muscle structural integrity (kelch protein 41b (klh41b), collagen α-1(XXVIII) chain (COL28A1), and cathepsin K (CTSK)) and protection against lipid oxidation (peroxiredoxin, superoxide dismutase 2 (SOD2), sestrin-1, Ubiquitin carboxyl-terminal hydrolase-10 (USP10)). A-to-G single-nucleotide polymorphism in β,β-carotene 15,15'-dioxygenase, and USP10 result in isoleucine-to-valine and proline-to-leucine non-synonymous amino acid substitutions, respectively. Our observation confirms that fillet color is a complex trait regulated by many genes involved in carotenoid metabolism, myoglobin homeostasis, protection against lipid oxidation, and maintenance of muscle structural integrity. The significant SNPs identified in this study could be prioritized via genomic selection in breeding programs to improve fillet color in rainbow trout.

Keywords: GWAS; fillet color; genes; genetic markers; rainbow trout.

Publication types

Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Animals
Carotenoids / metabolism
Genome-Wide Association Study
Lipids
Myoglobin / genetics
Oncorhynchus mykiss* / genetics
Oncorhynchus mykiss* / metabolism
beta-Carotene 15,15'-Monooxygenase / metabolism

Substances

Lipids
Myoglobin
Carotenoids
beta-Carotene 15,15'-Monooxygenase

Grants and funding

This study was supported by competitive grants No. 2014-67015-21602 and 2021-67015-33388 from the United States Department of Agriculture, National Institute of Food and Agriculture (M.S., T.L., B.K.), and by the USDA, Agricultural Research Service CRIS Project 1930-31000-010 “Utilizing Genetics and Physiology for Enhancing Cool- and Cold-Water Aquaculture Production” (T.L.). The content is solely the authors’ responsibility and does not necessarily represent the official views of any funding agents.