Conservation genomics of Atlantic salmon towards understanding adaptive trait differences for the management of endangered populations

加拿大基因组研究所的GRASP项目开发了一种新的基因表达微阵列，其中包含来自鲑科鱼类的16,000种不同基因。这导致了许多研究，比较了不同环境下鲑鱼不同组织的基因活性。然而，现有的研究并没有告诉我们在不同鲑鱼种群中观察到的基因表达变异（表达水平多态性：ELP）有多少是遗传的。最近的分子标记表明，芬迪内湾濒临灭绝的上鲑鱼河中有10%的小鲑鱼是该河流原生鲑鱼和从欧洲水产养殖品种逃出来的鲑鱼之间的F1杂交后代。在我们项目的第一部分，这些F1“跨大西洋”个体将与亲本群体中的一个回交，以创建两个大的全同胞研究家族，这些研究家族将分离出每个原始亲本菌株特有的等位基因。这些回交家族将使我们能够使用一种强大的统计学方法来识别基因，这些基因的elp与我们每个全同胞家族中个体的形态、生理和生活史特征的特定值密切相关。在我们项目的第二部分，我们将通过比较这些基因的DNA序列来验证这些相关性具有遗传基础，并寻找在两个亲本种群之间序列变化的称为snp（单核苷酸多态性）的位点。然后，我们将使用最有希望的SNP标记对濒危野生大西洋鲑鱼的尾片段进行基因型分析，这些鲑鱼被放在一个普通的孵化场环境中。这将使我们能够记录这些濒危鲑鱼种群在功能性状上的遗传差异，并可能有助于它们的保护。这些SNP遗传标记的开发最终将使水产养殖业能够在新不伦瑞克省授权使用的圣约翰水产养殖品系中进行标记辅助选择。

Genome Canada's GRASP project has developed a new gene expression microarray containing 16,000 different genes from salmonid fishes. This has resulted in many studies that compare gene activity in different tissues of salmon subject to different environments.  However, the existing studies do not tell us how much of the observed variation in gene expression (expression level polymorphism: ELP) among different salmon populations is genetic.  Recent molecular markers have shown that 10% of the smolts from the endangered Upper Salmon River run in the Inner Bay of Fundy are F1 hybrids between salmon native to this stream and escaped salmon from a European Aquacultural strain.  In the first part of our project these F1 "Trans Atlantic" individuals will be backcrossed back to one of the parental populations to create two large full sib research families that will be segregating for the alleles that are unique to each of the original parental strains.  These backcross families will enable us to use a statistically powerful method to identify genes whose ELPs that are strongly correlated with particular values of morphological, physiological and life history traits for individuals within each of our full sib families.  In the second part of our project we will verify that these correlations have a genetic basis by comparing the DNA sequences of these genes and look for sites called SNPs (single nucleotide polymorphisms) that vary in sequence between the two parental populations.  We will then use our most promising SNP markers to genotype tail clips from endangered wild Atlantic salmon that are held in a common hatchery environment.  This will enable us to document the genetic differences in functional traits among these endangered salmon populations and may assist in their conservation. Development of these SNP genetic markers will eventually enable the aquaculture industry to practise marker-assisted selection within the St. John's Aquaculture strain that is authorized for use in New Brunswick.