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. 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. 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.

中文翻译：

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全基因组测序鉴定出干扰素诱导蛋白 IFI6/IFI27-like 作为欧洲海鲈 VNN 抗性的一个强有力的候选基因

病毒性神经坏死 (VNN) 是一种影响欧洲海鲈鱼的主要疾病，了解 VNN 抗性背后的生物学机制对于养殖鱼类的福利和生产系统的可持续性非常重要。本研究的目的是确定与鲈鱼 VNN 抗性相关的基因组区域和基因。我们生成了一个包含 838,451 个单核苷酸多态性 (SNP) 的数据集，这些单核苷酸多态性 (SNP) 从欧洲海鲈的两个商业种群（A：2371 个个体和 B：3428 个个体）的亲代中通过全基因组测序 (WGS) 识别，具有二元生存表型记录在 VNN 挑战中。对于每个种群，三个队列通过浸泡进行红斑石斑鱼神经坏死病毒 (RGNNV) 攻击，并在 57K SNP 芯片上进行基因分型。在从父母那里估算出 WGS SNP 后，使用贝叶斯稀疏线性混合模型 (BSLMM) 绘制数量性状位点 (QTL)。我们发现了几个特定于不同连锁群 (LG) 上的一个种群的 QTL 区域，以及 LG12 上的一个 127-kb QTL 区域，由两个种群共享，包括编码棕榈酰转移酶的基因 ZDHHC14 和 IFI6/ IFI27-like，编码干扰素-α诱导蛋白。该 QTL 区域中最重要的 SNP 仅位于 IFI6/IFI27 样基因编码序列下游 1.9 kb。使用四个大家族的无关种群来验证 QTL 的效果。易感基因型的存活率在 A 和 B 群体中分别为 40.6% 和 45.4%，而抗性基因型的存活率为 66。种群 B 中为 2%，种群 A 中为 78%。我们已经确定了一个基因组区域，该区域携带一个对 VNN 具有抗性的主要 QTL，并且包括 ZDHHC14 和 IFI6/IFI27 样基因。干扰素途径的潜在参与，一种在几种生物体（鸡、人或鱼）中众所周知的抗病毒防御机制，在 VNN 感染的存活中特别令人感兴趣。我们的结果可以通过标记辅助基因组选择获得更具抗性的鱼，从而对海鲈育种计划产生重大改进。VNN 感染的存活率特别令人感兴趣。我们的结果可以通过标记辅助基因组选择获得更具抗性的鱼，从而对海鲈育种计划产生重大改进。VNN 感染的存活率特别令人感兴趣。我们的结果可以通过标记辅助基因组选择获得更具抗性的鱼，从而对海鲈育种计划产生重大改进。