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

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.

RNA-Seq analysis of the pyloric caecum, liver, and muscle reveals molecular mechanisms regulating fillet color in rainbow trout

“…This discrepancy might be due to differences in the design of the two experiments, i.e., absence of supplemental Astaxanthin in one group of fish in Schmeisser et al [ 22 ] compared to our study, where both the white and red fillet groups were fed supplemental Astaxanthin. Retinol dehydrogenase-7 was identified in a genome-wide association study as one of the genes influencing fillet color in rainbow trout [ 5 ].…”

“…Reactive oxygen species and oxidative stress can deteriorate lipids, adversely affecting fillet color [ 83 , 84 ]. A GWAS study identified several genes involved in myoglobin homeostasis and protection against lipid oxidation influencing fillet color in rainbow trout [ 5 ]. Such genes include cytochrome b5, ATP synthase subunit β, mitochondrial (ATP5F1B), calsequestrin, peroxiredoxin, superoxide dismutase, sestrin, and ubiquitin carboxyl-terminal hydrolase.…”

“…In aquaculture, synthetic carotenoids, especially Astaxanthin, are added as feed additives to provide similar fillet coloration. This characteristic reddish/pink fillet coloration is an important quality criterion that can influence consumers purchasing decisions [ 5 ]. It has been observed that only a small proportion (2–22%) of the supplied Astaxanthin is deposited and retained in the muscle of rainbow trout [ 6 , 7 ].…”