Genetic Basis for Resistance Against Viral Nervous Necrosis: GWAS and Potential of Genomic Prediction Explored in Farmed European Sea Bass (Dicentrarchus labrax)

Sergio Vela-Avitúa; Ingunn Thorland; Vasileios Bakopoulos; Kantham Papanna; Arkadios Dimitroglou; Eleftherios Kottaras; Papaharisis Leonidas; Bruno Guinand; Costas S Tsigenopoulos; Muhammad L Aslam

doi:10.3389/fgene.2022.804584

Genetic Basis for Resistance Against Viral Nervous Necrosis: GWAS and Potential of Genomic Prediction Explored in Farmed European Sea Bass (Dicentrarchus labrax)

Front Genet. 2022 Mar 25:13:804584. doi: 10.3389/fgene.2022.804584. eCollection 2022.

Affiliations

¹ Benchmark Genetics Norway AS (formerly Akvaforsk Genetics Center AS), Sunndalsøra, Norway.
² Laboratory of Ichthyology, Aquaculture and Diseases of Aquatic Animals, Department of Marine Sciences, University of The Aegean, Mytilene, Greece.
³ Nireus Aquaculture SA., Koropi, Greece.
⁴ CNRS, IRD, EPHE, ISEM, Université de Montpellier, Montpellier, France.
⁵ Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Institute of Marine Biology, Heraklion, Greece.
⁶ Nofima AS, Tromsø, Norway.

Abstract

Viral nervous necrosis (VNN) is an infectious disease caused by the red-spotted grouper nervous necrosis virus (RGNNV) in European sea bass and is considered a serious concern for the aquaculture industry with fry and juveniles being highly susceptible. To understand the genetic basis for resistance against VNN, a survival phenotype through the challenge test against the RGNNV was recorded in populations from multiple year classes (YC2016 and YC2017). A total of 4,851 individuals from 181 families were tested, and a subset (n∼1,535) belonging to 122 families was genotyped using a ∼57K Affymetrix Axiom array. The survival against the RGNNV showed low to moderate heritability with observed scale estimates of 0.18 and 0.25 obtained using pedigree vs. genomic information, respectively. The genome-wide association analysis showed a strong signal of quantitative trait loci (QTL) at LG12 which explained ∼33% of the genetic variance. The QTL region contained multiple genes (ITPK1, PLK4, HSPA4L, REEP1, CHMP2, MRPL35, and SCUBE) with HSPA4L and/or REEP1 genes being highly relevant with a likely effect on host response in managing disease-associated symptoms. The results on the accuracy of predicting breeding values presented 20-43% advantage in accuracy using genomic over pedigree-based information which varied across model types and applied validation schemes.

Keywords: VNN; genome-wide association analysis; genomic prediction; heritability; nervous necrosis virus; quantitative trait loci; single nucleotide polymorphisms; viral nervous necrosis.