Abstract
One of the top priorities of the aquaculture industry is the genetic improvement of economically important traits in fish, such as those related to processing and quality. However, the accuracy of genetic evaluations has been hindered by a lack of data on such traits from a sufficiently large population of animals. The objectives of this study were thus threefold: (i) to estimate genetic parameters of growth-, yield-, and quality-related traits in rainbow trout (Oncorhynchus mykiss) using three different phenotyping technologies [invasive and non-invasive: microwave-based, digital image analysis, and magnetic resonance imaging (MRI)], (ii) to detect quantitative trait loci (QTLs) associated with these traits, and (iii) to identify candidate genes present within these QTL regions. Our study collected data from 1,379 fish on growth, yield-related traits (body weight, condition coefficient, head yield, carcass yield, headless gutted carcass yield), and quality-related traits (total fat, percentage of fat in subcutaneous adipose tissue, percentage of fat in flesh, flesh colour); genotypic data were then obtained for all fish using the 57K SNP Axiom® Trout Genotyping array. Heritability estimates for most of the 14 traits examined were moderate to strong, varying from 0.12 to 0.67. Most traits were clearly polygenic, but our genome-wide association studies (GWASs) identified two genomic regions on chromosome 8 that explained up to 10% of the genetic variance (cumulative effects of two QTLs) for several traits (weight, condition coefficient, subcutaneous and total fat content, carcass and headless gutted carcass yields). For flesh colour traits, six QTLs explained 1–4% of the genetic variance. Within these regions, we identified several genes (htr1, gnpat, ephx1, bcmo1, and cyp2x) that have been implicated in adipogenesis or carotenoid metabolism, and thus represent good candidates for further functional validation. Finally, of the three techniques used for phenotyping, MRI demonstrated particular promise for measurements of fat content and distribution, while the digital image analysis-based approach was very useful in quantifying colour-related traits. This work provides new insights that may aid the development of commercial breeding programmes in rainbow trout, specifically with regard to the genetic improvement of yield and flesh-quality traits as well as the use of invasive and/or non-invasive technologies to predict such traits.
Highlights
Aquaculture produces high-quality animal protein that is low in saturated fat, ideal for satisfying increased global demand
To estimate lipid content and its distribution, X-ray computed tomography (CT) and magnetic resonance imaging (MRI) can be applied to a representative cutlet and the results evaluated using image analysis, an approach that has already been used for the phenotypic estimation of fat content in fish (Gjerde and Martens, 1987; Kolstad et al, 2004; Marty-Mahé et al, 2004; Toussaint et al, 2005; Mathiassen et al, 2011; Collewet et al, 2013; Picaud et al, 2016)
This work provides new insights into the genetics of traits associated with yield and flesh quality in rainbow trout which can be applied to commercial breeding
Summary
Aquaculture produces high-quality animal protein that is low in saturated fat, ideal for satisfying increased global demand. Most of animals are female, diploid or triploid, and reared for the production of fillets, which are consumed fresh or smoked (Vandeputte et al, 2019) For both economic and environmental reasons, the main challenge in trout production is promoting efficient growth while maintaining the quality of the fillet. Consumers are mainly concerned with fillet or flesh quality, followed by fat content, colour, texture, and flavour (Rasmussen et al, 2001). For both parties, the heterogeneous distribution of lipids within a fish has major effects on product quality (Katikou et al, 2001). Subcutaneous adipose tissue is discarded during fillet trimming and is negatively linked to fillet yield, while the quantity of lipids in the flesh has strong effects on the sensory quality of fish, such as texture and flavour (Grigorakis, 2007), and its overall acceptability to consumers (Katikou et al, 2001)
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