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

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 accumula...

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Autores principales: Ahmed, Ridwan O., Ali, Ali, Al-Tobasei, Rafet, Leeds, Tim, Kenney, Brett, Salem, Mohamed
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9332390/
https://www.ncbi.nlm.nih.gov/pubmed/35893068
http://dx.doi.org/10.3390/genes13081331
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author Ahmed, Ridwan O.
Ali, Ali
Al-Tobasei, Rafet
Leeds, Tim
Kenney, Brett
Salem, Mohamed
author_facet Ahmed, Ridwan O.
Ali, Ali
Al-Tobasei, Rafet
Leeds, Tim
Kenney, Brett
Salem, Mohamed
author_sort Ahmed, Ridwan O.
collection PubMed
description 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.
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spelling pubmed-93323902022-07-29 Weighted Single-Step GWAS Identifies Genes Influencing Fillet Color in Rainbow Trout Ahmed, Ridwan O. Ali, Ali Al-Tobasei, Rafet Leeds, Tim Kenney, Brett Salem, Mohamed Genes (Basel) Article 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. MDPI 2022-07-26 /pmc/articles/PMC9332390/ /pubmed/35893068 http://dx.doi.org/10.3390/genes13081331 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Ahmed, Ridwan O.
Ali, Ali
Al-Tobasei, Rafet
Leeds, Tim
Kenney, Brett
Salem, Mohamed
Weighted Single-Step GWAS Identifies Genes Influencing Fillet Color in Rainbow Trout
title Weighted Single-Step GWAS Identifies Genes Influencing Fillet Color in Rainbow Trout
title_full Weighted Single-Step GWAS Identifies Genes Influencing Fillet Color in Rainbow Trout
title_fullStr Weighted Single-Step GWAS Identifies Genes Influencing Fillet Color in Rainbow Trout
title_full_unstemmed Weighted Single-Step GWAS Identifies Genes Influencing Fillet Color in Rainbow Trout
title_short Weighted Single-Step GWAS Identifies Genes Influencing Fillet Color in Rainbow Trout
title_sort weighted single-step gwas identifies genes influencing fillet color in rainbow trout
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9332390/
https://www.ncbi.nlm.nih.gov/pubmed/35893068
http://dx.doi.org/10.3390/genes13081331
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