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

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 genomewide 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.

Genetic Parameters and Genome-Wide Association Studies of Quality Traits Characterised Using Imaging Technologies in Rainbow Trout, Oncorhynchus mykiss

“…In this study, we identified new QTLs associated with production and flesh-quality traits in rainbow trout. However, our work is consistent with previous reports ( Gonzalez-Pena et al, 2016 ; Salem et al, 2018 ; Ali et al, 2020a ) in characterising the vast majority of these traits as polygenic.…”

“…Additionally, an older study detected QTLs for body weight and condition factor on linkage groups RT-9 (corresponding to Omy12) and RT-27 (corresponding to Omy2) ( Wringe et al, 2010 ). More recently, QTLs for muscle fat and moisture content were identified on chromosomes 19 and 29 in rainbow trout ( Ali et al, 2019 , 2020a ). In farmed Atlantic salmon, significant QTLs were identified on chromosomes 13, 18, and 20 with effects on growth and yield-related traits ( Tsai et al, 2015 ) and on chromosome 9 and 10 for fat content ( Sodeland et al, 2013 ).…”

“…In rainbow trout, GWAS has been used to identify significant QTLs associated with such traits of interest as growth or disease resistance ( Laghari et al, 2014 ; Kocmarek et al, 2015 ; Liu et al, 2015 ; Abdelrahman et al, 2017 ; Ashton et al, 2017 ; Vallejo et al, 2017 ; Fraslin et al, 2018 ; Reis Neto et al, 2019 ; Ali et al, 2020b ). Recently, studies have begun to focus on quality traits like fillet yield ( Gonzalez-Pena et al, 2016 ; Al-Tobasei et al, 2017 ), muscle yield ( Salem et al, 2018 ), skinned and trimmed fillet yield ( Al-Tobasei et al, 2020 ), shear force and fillet firmness ( Al-Tobasei et al, 2017 , 2020 ; Ali et al, 2019 ), fillet whiteness as determined by L ∗ a ∗ b ∗ characteristics ( Al-Tobasei et al, 2017 ), and intramuscular fat content and moisture ( Ali et al, 2020a ). However, these studies were carried out on two experimental lines of trout that had been previously selected for growth or for resistance to Flavobacterium psychrophilum by the NCCCWA breeding program in the United States ( Leeds et al, 2016 ) and in China ( Hu et al, 2020 ).…”

Identification of candidate genes on the basis of SNP by time-lagged heat stress interactions for milk production traits in German Holstein cattle

“…However, no study reported a relationship between the three genes and TSCS. The gene ABCC9 harbors the most significant SNPs for production traits [ 41 ], the gene WDR7 is associated with sperm motility and concentration in Holstein-Friesian bulls [ 52 ], and the gene TXNL1 has an effect on moisture content in rainbow trout [ 53 ]. The response to oxygen-containing compound and the G-proteifan-coupled receptors signaling pathway were significantly detected based on all candidate genes for main effects.…”

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

“…GWA studies take advantage of linkage disequilibrium between SNP markers and genetic loci controlling a trait of interest. GWA studies have been conducted in the rainbow trout breeding program at the National Center for Cool- and Cold-Water Aquaculture (NCCCWA) for growth [ 6 ], muscle yield [ 7 ], intramuscular fat [ 8 ], fillet firmness [ 9 ], and disease resistance [ 10 ]. Another essential trait that requires attention is the fillet color—targeted in this study.…”