Whole‐genome sequencing identifies interferon-induced protein IFI6/IFI27-like as a strong candidate gene for VNN resistance in European sea bass

Type Article
Date 2023-05
Language English
Author(s) Delpuech EmilieORCID2, 9, Vandeputte MarcORCID2, 9, Morvezen Romain3, Bestin Anastasia3, Besson Mathieu3, Brunier Joseph4, Bajek Aline4, Imarazene Boudjema5, François Yoannah3, 6, Bouchez Olivier7, Cousin XavierORCID2, 9, Poncet Charles8, Morin Thierry6, Bruant Jean-Sébastien5, Chatain Beatrice1, Haffray Pierrick3, Phocas Florence2, Allal FrancoisORCID1
Affiliation(s) 1 : MARBEC, Univ. Montpellier, CNRS, Ifremer, IRD, INRAE, 34250, Palavas-Les-Flots, France
2 : Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
3 : SYSAAF, Station LPGP/INRAE, Campus de Beaulieu, 35042, Rennes, France
4 : Ecloserie Marine de Gravelines-Ichtus, Gloria Maris Group, 59273, Gravelines, France
5 : Fermes Marines Du Soleil, 17840, La Brée Les Bains, France
6 : ANSES, Unit Virology, Immunology and Ecotoxicology of Fish, Technopôle Brest-Iroise, 29280, Plouzané, France
7 : US 1426, GeT-PlaGe, INRAE, Genotoul, Castanet-Tolosan, France
8 : INRAE-UCA, UMR 1095 GDEC, 63000, Clermont-Ferrand, France
9 : MARBEC, Univ. Montpellier, CNRS, Ifremer, IRD, INRAE, 34250, Palavas-Les-Flots, France
Source Genetics Selection Evolution (0999-193X) (Springer Science and Business Media LLC), 2023-05 , Vol. 55 , N. 1 , P. 30 (12p.)
DOI 10.1186/s12711-023-00805-2

Background Viral nervous necrosis (VNN) is a major disease that affects European sea bass, and understanding the biological mechanisms that underlie VNN resistance is important for the welfare of farmed fish and sustainability of production systems. The aim of this study was to identify genomic regions and genes that are associated with VNN resistance in sea bass. Results We generated a dataset of 838,451 single nucleotide polymorphisms (SNPs) identified from whole-genome sequencing (WGS) in the parental generation of two commercial populations (A: 2371 individuals and B: 3428 individuals) of European sea bass with phenotypic records for binary survival in a VNN challenge. For each population, three cohorts were submitted to a red-spotted grouper nervous necrosis virus (RGNNV) challenge by immersion and genotyped on a 57K SNP chip. After imputation of WGS SNPs from their parents, quantitative trait loci (QTL) were mapped using a Bayesian sparse linear mixed model (BSLMM). We found several QTL regions that were specific to one of the populations on different linkage groups (LG), and one 127-kb QTL region on LG12 that was shared by both populations and included the genes ZDHHC14, which encodes a palmitoyltransferase, and IFI6/IFI27-like, which encodes an interferon-alpha induced protein. The most significant SNP in this QTL region was only 1.9 kb downstream of the coding sequence of the IFI6/IFI27-like gene. An unrelated population of four large families was used to validate the effect of the QTL. Survival rates of susceptible genotypes were 40.6% and 45.4% in populations A and B, respectively, while that of the resistant genotype was 66.2% in population B and 78% in population A. Conclusions We have identified a genomic region that carries a major QTL for resistance to VNN and includes the ZDHHC14 and IFI6/IFI27-like genes. The potential involvement of the interferon pathway, a well-known anti-viral defense mechanism in several organisms (chicken, human, or fish), in survival to VNN infection is of particular interest. Our results can lead to major improvements for sea bass breeding programs through marker-assisted genomic selection to obtain more resistant fish.

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Publisher's official version 12 1 MB Open access
Figure S1. PCA on genotypes of commercial populations (pop A and pop B) and wild populations in the Atlantic (Atl) and Eastern Mediterranean (East-Med)..... 203 KB Open access
Table S1. Number of SNPs removed after several quality filters. Details of the number of SNPs removed with quality controls applied on whole-genome sequences and 57K SNP chip data. 16 KB Open access
Additional file 3: Flanking 50-bp sequences for the top associated SNPs in LG12_QTL_2. Genomic sequences flanking the IFI6/IFI27-like and ZDHHC14 SNPs computed from Dicentrarchus labrax genome ... 15 KB Open access
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Delpuech Emilie, Vandeputte Marc, Morvezen Romain, Bestin Anastasia, Besson Mathieu, Brunier Joseph, Bajek Aline, Imarazene Boudjema, François Yoannah, Bouchez Olivier, Cousin Xavier, Poncet Charles, Morin Thierry, Bruant Jean-Sébastien, Chatain Beatrice, Haffray Pierrick, Phocas Florence, Allal Francois (2023). Whole‐genome sequencing identifies interferon-induced protein IFI6/IFI27-like as a strong candidate gene for VNN resistance in European sea bass. Genetics Selection Evolution, 55(1), 30 (12p.). Publisher's official version : https://doi.org/10.1186/s12711-023-00805-2 , Open Access version : https://archimer.ifremer.fr/doc/00835/94739/