Brown trout is one of the most widespread fresh-water fish species in Europe. The evolutionary history of and phylogenetic relationships between brown trout populations are complex, and this is especially true for Italian populations, which are heavily influenced in different ways by stocking practices. The characterization of the genetic structure of Italian brown trout populations may give information on the risk of losing endemic Italian populations due to lack of genetic diversity or to admixture with stocking populations. The identification of signatures of selection, and the information deriving from dense genotyping data will help genotype-informed breeding programs. We used a ddRAD-seq approach to obtain more than 100,000 single nucleotide polymorphisms (SNPs), and to characterize the population structure and signatures of selection in 90 brown trout samples. Italian brown trout populations are genetically differentiated, although the stocking practices have introduced strong admixture in endemic Italian trout, especially with the Atlantic lineage. Most of the analysed populations showed high levels of kinship and inbreeding. We detected putative signatures of selection using different approaches, and investigated if the regions were enriched for functional categories. Several regions putatively under selection and characterized by a reduction in heterozygosity across all the studied populations are enriched for genes involved in the response to viral infections. Our results, which show evidence of admixture with the Atlantic lineage (commonly used for stocking), confirm the need for controlling stocking practices, in order to avoid the erosion of the endemic gene pool; given the apparently high levels of kinship and inbreeding in local populations, our results also show the need to take action for increasing gene diversity. In addition, we used the genetically-distinct lineages to detect signatures of selection and we identified putative signatures of selection in several regions associated with resistance to infectious diseases. These constitute candidate regions for the study of resistance to infections in wild and farmed trout.

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ddRAD-seq 揭示了意大利褐鳟的遗传结构并检测了选择信号

褐鳟是欧洲分布最广的淡水鱼种之一。褐鳟种群的进化历史和系统发育关系很复杂，意大利种群尤其如此，它们在不同方面受到放养做法的严重影响。意大利褐鳟种群遗传结构的特征可能会提供有关由于缺乏遗传多样性或与放养种群混合而失去意大利地方性种群的风险的信息。选择特征的识别以及来自密集基因分型数据的信息将有助于基因型育种计划。我们使用 ddRAD-seq 方法获得了超过 100,000 个单核苷酸多态性 (SNP)，并描述 90 个褐鳟鱼样本的种群结构和选择特征。意大利褐鳟种群在遗传上存在差异，尽管放养做法在意大利特有的鳟鱼中引入了强烈的混合物，特别是与大西洋血统。大多数被分析的种群显示出高水平的亲属关系和近亲繁殖。我们使用不同的方法检测了推定的选择特征，并调查了这些区域是否丰富了功能类别。几个被推定在选择下的区域，其特征是所有研究人群的杂合性降低，富含参与病毒感染反应的基因。我们的结果显示了与大西洋血统（通常用于放养）混合的证据，确认有必要控制放养做法，以避免地方性基因库的侵蚀；鉴于当地人口的亲缘关系和近亲繁殖水平明显较高，我们的结果还表明需要采取行动增加基因多样性。此外，我们使用遗传上不同的谱系来检测选择的特征，并在与传染病抗性相关的几个区域中确定了推定的选择特征。这些构成了研究野生和养殖鳟鱼感染抗性的候选区域。我们使用遗传上不同的谱系来检测选择的特征，并在与传染病抗性相关的几个区域中确定了推定的选择特征。这些构成了研究野生和养殖鳟鱼感染抗性的候选区域。我们使用遗传上不同的谱系来检测选择的特征，并在与传染病抗性相关的几个区域中确定了推定的选择特征。这些构成了研究野生和养殖鳟鱼感染抗性的候选区域。