Genome-wide association studies for resistance to viral nervous necrosis in three populations of European sea bass (Dicentrarchus labrax) using a novel 57 k SNP array DlabChip

Type Article
Date 2021-01
Language English
Author(s) Griot Ronan1, 2, 3, Allal FrancoisORCID3, Phocas F.2, Brard-Fudulea S.4, Morvezen R.1, Bestin A.1, Haffray P.1, François Yoannah1, Morin Thierry6, Poncet C.5, Vergnet Alain3, Cariou S.7, Brunier J.8, Bruant J.S.7, Peyrou B.8, Gagnaire P.A.9, Vandeputte MarcORCID2, 10
Affiliation(s) 1 : SYSAAF, Station LPGP/INRAE, Campus de Beaulieu, 35042 Rennes, France
2 : Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350 Jouy-en-Josas, France
3 : MARBEC, Univ. Montpellier, Ifremer, CNRS, IRD, 34250 Palavas-les-Flots, France
4 : SYSAAF, UMR BOA, Centre INRAE Val de Loire, 37380 Nouzilly, France
5 : INRAE-UCA, UMR GDEC, Clermont-Ferrand, France
6 : ANSES, Ploufragan-Plouzané-Niort Laboratory, Viral Fish Diseases Unit, National Reference Laboratory for Regulated Fish Diseases, Technopôle Brest-Iroise, 29280 Plouzané, France
7 : Ferme Marine Du Douhet, 17840 La Brée Les Bains, France
8 : Ecloserie Marine de Gravelines-Ichtus, 59273 Gravelines, France
9 : ISEM, Université de Montpellier, CNRS-IRD-EPHE-, UM, France
10 : MARBEC, Univ. Montpellier, Ifremer, CNRS, IRD, 34250 Palavas-les-Flots, France
Source Aquaculture (0044-8486) (Elsevier BV), 2021-01 , Vol. 530 , P. 735930 (10p.)
DOI 10.1016/j.aquaculture.2020.735930
WOS© Times Cited 5
Keyword(s) Disease resistance, VNN, Fish, SNP array, QTL, GWAS, Linkage map
Abstract

Viral Nervous Necrosis (VNN) is a major threat for the European sea bass (Dicentrarchus labrax) aquaculture industry. The improvement of disease resistance through selective breeding is a promising option to reduce outbreaks. With the development of high-throughput genotyping technologies, identification of genomic regions involved in the resistance could improve the efficiency of selective breeding. The aim of this study was to identify quantitative trait loci (QTL) involved in VNN resistance and to quantify their effect.

Four experimental backcross families comprising 378, 454, 291 and 211 individuals and two commercial populations A and B comprising 1027 and 1042 individuals obtained from partial factorial crosses (59♂ x 20♀ for pop A; 39♂ x 14♀ for pop B) were submitted to a redspotted grouper nervous necrosis virus (RGNNV) challenge by bath. A high-density single nucleotide polymorphism (SNP) chip panel was designed to develop the ThermoFisher Axiom™ 57 k SNP DlabChip, which was used for genotyping all individuals and building a high quality linkage map. In the backcross families, composite interval mapping was performed on 30,917, 23,592, 30,656 and 31,490 markers, respectively. In the commercial populations, 40,263 markers in pop A and 41,166 markers in pop B were used to perform genome-wide association studies (GWAS) using a GBLUP and a BayesCπ approach.

One QTL was identified on chromosome LG12 in three of the four experimental backcross families, and one additional QTL on LG8 was detected in only one family. In commercial populations, QTL mapping revealed a total of seven QTLs, among which the previously mentioned QTL on LG12 was detected in both. This QTL, which was mapped to an interval of 3.45 cM, explained 9.21% of the total genetic variance in pop A, while other identified QTLs individually explained less than 1% of the total genetic variance.

The identification of QTL regions involved in VNN resistance in European sea bass, with one having a strong effect, should have a great impact on the aquaculture industry. Future work could focus on the fine mapping of the causal mutation present on LG12 using whole genome sequencing.

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Griot Ronan, Allal Francois, Phocas F., Brard-Fudulea S., Morvezen R., Bestin A., Haffray P., François Yoannah, Morin Thierry, Poncet C., Vergnet Alain, Cariou S., Brunier J., Bruant J.S., Peyrou B., Gagnaire P.A., Vandeputte Marc (2021). Genome-wide association studies for resistance to viral nervous necrosis in three populations of European sea bass (Dicentrarchus labrax) using a novel 57 k SNP array DlabChip. Aquaculture, 530, 735930 (10p.). Publisher's official version : https://doi.org/10.1016/j.aquaculture.2020.735930 , Open Access version : https://archimer.ifremer.fr/doc/00648/76027/