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

Type Article
Date 2021-02
Language English
Author(s) Blay Carole1, Haffray Pierrick2, Bugeon Jérôme3, D’ambrosio Jonathan1, 2, Dechamp Nicolas1, Collewet Guylaine4, Enez Florian2, Petit Vincent5, Cousin XavierORCID1, 6, Corraze Geneviève7, Phocas Florence1, Dupont-Nivet Mathilde1
Affiliation(s) 1 : Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
2 : SYSAAF, Station LPGP-INRAE, Rennes, France
3 : INRAE, LPGP, Rennes, France
4 : INRAE, OPAALE, Rennes, France
5 : Les Sources de l’Avance, Pissos, France
6 : MARBEC, University of Montpellier, CNRS, Ifremer, IRD, Palavas-les-Flots, France
7 : INRAE, University of Pau & Pays Adour, E2S UPPA, UMR 1419 NuMéA, Saint-Pée-sur-Nivelle, France
Source Frontiers In Genetics (1664-8021) (Frontiers Media SA), 2021-02 , Vol. 12 , P. 639223 (17p.)
DOI 10.3389/fgene.2021.639223
WOS© Times Cited 10
Keyword(s) aquaculture, fat content, flesh colour, magnetic resonance imaging, Fatmeter, computer vision, genetic correlations, QTL

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.

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Blay Carole, Haffray Pierrick, Bugeon Jérôme, D’ambrosio Jonathan, Dechamp Nicolas, Collewet Guylaine, Enez Florian, Petit Vincent, Cousin Xavier, Corraze Geneviève, Phocas Florence, Dupont-Nivet Mathilde (2021). Genetic Parameters and Genome-Wide Association Studies of Quality Traits Characterised Using Imaging Technologies in Rainbow Trout, Oncorhynchus mykiss. Frontiers In Genetics, 12, 639223 (17p.). Publisher's official version : , Open Access version :