FN Archimer Export Format
PT J
TI Whole‐genome sequencing identifies interferon-induced protein IFI6/IFI27-like as a strong candidate gene for VNN resistance in European sea bass
BT 
AF 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
AS 1:2,9;2:2,9;3:3;4:3;5:3;6:4;7:4;8:5;9:3,6;10:7;11:2,9;12:8;13:6;14:5;15:1;16:3;17:2;18:1;
FF 1:;2:;3:;4:;5:;6:;7:;8:;9:;10:;11:;12:;13:;14:;15:PDG-RBE-MARBEC-LAAAS;16:;17:;18:PDG-RBE-MARBEC-LAAAS;
C1 MARBEC, Univ. Montpellier, CNRS, Ifremer, IRD, INRAE, 34250, Palavas-Les-Flots, France
   Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
   SYSAAF, Station LPGP/INRAE, Campus de Beaulieu, 35042, Rennes, France
   Ecloserie Marine de Gravelines-Ichtus, Gloria Maris Group, 59273, Gravelines, France
   Fermes Marines Du Soleil, 17840, La Brée Les Bains, France
   ANSES, Unit Virology, Immunology and Ecotoxicology of Fish, Technopôle Brest-Iroise, 29280, Plouzané, France
   US 1426, GeT-PlaGe, INRAE, Genotoul, Castanet-Tolosan, France
   INRAE-UCA, UMR 1095 GDEC, 63000, Clermont-Ferrand, France
   MARBEC, Univ. Montpellier, CNRS, Ifremer, IRD, INRAE, 34250, Palavas-Les-Flots, France
C2 IFREMER, FRANCE
   INRAE, FRANCE
   SYSAAF, FRANCE
   ECLOSERIE MARINE GRAVELINES ICHTUS, FRANCE
   FERMES MARINES SOLEIL, FRANCE
   ANSES, FRANCE
   INRAE, FRANCE
   INRAE, FRANCE
   INRAE, FRANCE
SI PALAVAS
SE PDG-RBE-MARBEC-LAAAS
UM MARBEC
IN WOS Ifremer UMR
   WOS Cotutelle UMR
   DOAJ
   copubli-france
   copubli-p187
IF 4.1
TC 1
UR https://archimer.ifremer.fr/doc/00835/94739/102213.pdf
   https://archimer.ifremer.fr/doc/00835/94739/102214.docx
   https://archimer.ifremer.fr/doc/00835/94739/102215.xlsx
   https://archimer.ifremer.fr/doc/00835/94739/102216.docx
LA English
DT Article
AB 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. 
PY 2023
PD MAY
SO Genetics Selection Evolution
SN 0999-193X
PU Springer Science and Business Media LLC
VL 55
IS 1
UT 000981572100001
DI 10.1186/s12711-023-00805-2
ID 94739
ER

EF