Genetic architecture and genomic selection of fatty acid composition predicted by Raman spectroscopy in rainbow trout

Type Article
Date 2021-11
Language English
Author(s) Blay Carole1, Haffray Pierrick2, D’ambrosio Jonathan1, 2, Prado EnoraORCID3, Dechamp Nicolas1, Nazabal Virginie3, Bugeon Jérôme4, Enez Florian2, Causeur David5, Eklouh-Molinier Christophe2, Petit Vincent6, Phocas Florence1, Corraze Geneviève7, Dupont-Nivet Mathilde1
Affiliation(s) 1 : Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
2 : SYSAAF, Station LPGP-INRAE, Rennes, France
3 : University of Rennes, CNRS, ISCR – UMR 6226, ScanMAT – UMS 2001, Rennes, France
4 : INRAE, LPGP, Rennes, France
5 : Laboratoire de Mathématiques Appliquées, IRMAR, Agrocampus Ouest, Rennes, France
6 : Les Sources de l’Avance, Pissos, France
7 : INRAE, University of Pau & Pays Adour, E2S UPPA, UMR1419 NuMéA, St Pée sur, Nivelle, France
Source Bmc Genomics (1471-2164) (Springer Science and Business Media LLC), 2021-11 , Vol. 22 , N. 1 , P. 788 (19p.)
DOI 10.1186/s12864-021-08062-7
WOS© Times Cited 8
Keyword(s) Fish, Genomic selection, QTL, GWAS, Fatty acid, Raman, Genetic correlations, Accuracy
Abstract

Background

In response to major challenges regarding the supply and sustainability of marine ingredients in aquafeeds, the aquaculture industry has made a large-scale shift toward plant-based substitutions for fish oil and fish meal. But, this also led to lower levels of healthful n−3 long-chain polyunsaturated fatty acids (PUFAs)—especially eicosapentaenoic (EPA) and docosahexaenoic (DHA) acids—in flesh. One potential solution is to select fish with better abilities to retain or synthesise PUFAs, to increase the efficiency of aquaculture and promote the production of healthier fish products. To this end, we aimed i) to estimate the genetic variability in fatty acid (FA) composition in visceral fat quantified by Raman spectroscopy, with respect to both individual FAs and groups under a feeding regime with limited n-3 PUFAs; ii) to study the genetic and phenotypic correlations between FAs and processing yields- and fat-related traits; iii) to detect QTLs associated with FA composition and identify candidate genes; and iv) to assess the efficiency of genomic selection compared to pedigree-based BLUP selection.

Results

Proportions of the various FAs in fish were indirectly estimated using Raman scattering spectroscopy. Fish were genotyped using the 57 K SNP Axiom™ Trout Genotyping Array. Following quality control, the final analysis contained 29,652 SNPs from 1382 fish. Heritability estimates for traits ranged from 0.03 ± 0.03 (n-3 PUFAs) to 0.24 ± 0.05 (n-6 PUFAs), confirming the potential for genomic selection. n-3 PUFAs are positively correlated to a decrease in fat deposition in the fillet and in the viscera but negatively correlated to body weight. This highlights the potential interest to combine selection on FA and against fat deposition to improve nutritional merit of aquaculture products. Several QTLs were identified for FA composition, containing multiple candidate genes with indirect links to FA metabolism. In particular, one region on Omy1 was associated with n-6 PUFAs, monounsaturated FAs, linoleic acid, and EPA, while a region on Omy7 had effects on n-6 PUFAs, EPA, and linoleic acid. When we compared the effectiveness of breeding programmes based on genomic selection (using a reference population of 1000 individuals related to selection candidates) or on pedigree-based selection, we found that the former yielded increases in selection accuracy of 12 to 120% depending on the FA trait.

Conclusion

This study reveals the polygenic genetic architecture for FA composition in rainbow trout and confirms that genomic selection has potential to improve EPA and DHA proportions in aquaculture species.

Full Text
File Pages Size Access
Publisher's official version 19 2 MB Open access
Additional file 1. Fatty acid composition of the two final diets (% total FAs). 14 KB Open access
Additional file 2. Estimates of phenotypic correlations between proportions of fatty acids and production or quality traits. 15 KB Open access
Additional file 3. Candidate genes from the NCBI Oncorhynchus mykiss Annotation Release 100 (GCF_002163495.1) that were located within the confidence or credibility intervals estimated using BCπ ... 60 KB Open access
Additional file 4. Summary statistics for 11 production and quality traits in rainbow trout. 15 KB Open access
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How to cite 

Blay Carole, Haffray Pierrick, D’ambrosio Jonathan, Prado Enora, Dechamp Nicolas, Nazabal Virginie, Bugeon Jérôme, Enez Florian, Causeur David, Eklouh-Molinier Christophe, Petit Vincent, Phocas Florence, Corraze Geneviève, Dupont-Nivet Mathilde (2021). Genetic architecture and genomic selection of fatty acid composition predicted by Raman spectroscopy in rainbow trout. Bmc Genomics, 22(1), 788 (19p.). Publisher's official version : https://doi.org/10.1186/s12864-021-08062-7 , Open Access version : https://archimer.ifremer.fr/doc/00737/84948/