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™ 57k 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.

中文翻译：

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使用新型 57 k SNP 阵列 DlabChip 在三个欧洲鲈鱼（Dicentrarchus labrax）种群中对病毒性神经坏死抗性的全基因组关联研究

摘要 病毒性神经坏死（VNN）是欧洲鲈鱼（Dicentrarchus labrax）水产养殖业的主要威胁。通过选择性育种提高抗病性是减少疫情爆发的一个有前景的选择。随着高通量基因分型技术的发展，鉴定参与抗性的基因组区域可以提高选育效率。本研究的目的是确定涉及 VNN 抗性的数量性状基因座 (QTL) 并量化其影响。四个实验回交家系包括 378、454、291 和 211 个个体和两个商业群体 A 和 B，包括从部分因子杂交获得的 1027 和 1042 个个体（群体 A 为 59♂ x 20♀；39♂ x 14♀ 的流行 B) 被提交给红斑石斑鱼神经坏死病毒 (RGNNV) 洗澡。高密度单核苷酸多态性 (SNP) 芯片面板旨在开发 ThermoFisher Axiom™ 57k SNP DlabChip，用于对所有个体进行基因分型并构建高质量的连锁图。在回交家族中，分别对 30,917、23,592、30,656 和 31,490 个标记进行了复合区间作图。在商业人群中，pop A 中的 40,263 个标记和 pop B 中的 41,166 个标记用于使用 GBLUP 和 BayesCπ 方法进行全基因组关联研究 (GWAS)。在四个实验回交家族中的三个家族中，在 LG12 染色体上发现了一个 QTL，在 LG8 上仅在一个家族中检测到了一个额外的 QTL。在商业人群中，QTL定位共发现7个QTL，其中前文提到的LG12上的QTL在两者中均被检测到。该 QTL 映射到 3.45 cM 的区间，解释了 pop A 中总遗传方差的 9.21%，而其他已鉴定的 QTL 单独解释了总遗传方差的不到 1%。欧洲鲈鱼VNN抗性中涉及的QTL区域的鉴定，具有很强的作用，应该对水产养殖业产生很大的影响。未来的工作可以集中在使用全基因组测序对 LG12 上存在的因果突变进行精细定位。而其他已鉴定的 QTL 单独解释了不到总遗传变异的 1%。欧洲鲈鱼VNN抗性中涉及的QTL区域的鉴定，具有很强的作用，应该对水产养殖业产生很大的影响。未来的工作可以集中在使用全基因组测序对 LG12 上存在的因果突变进行精细定位。而其他已鉴定的 QTL 单独解释了不到总遗传变异的 1%。欧洲鲈鱼VNN抗性中涉及的QTL区域的鉴定，具有很强的作用，应该对水产养殖业产生很大的影响。未来的工作可以集中在使用全基因组测序对 LG12 上存在的因果突变进行精细定位。