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

加拿大基因组计划的GRAPH项目开发了一种新的基因表达微阵列，包含16,000个来自鲑鱼的不同基因。这导致了许多研究比较不同环境下鲑鱼不同组织中的基因活性。现有的研究没有告诉我们，观察到的不同鲑鱼种群之间的基因表达差异(表达水平多态：ELP)有多少是遗传的。最近的分子标记表明，来自芬迪内湾的濒危上游鲑鱼河的臭味中，有10%是来自这条河流的原产鲑鱼和从欧洲水产养殖品系逃逸的鲑鱼之间的F1杂交。在我们项目的第一部分，这些F1“跨大西洋”个体将回交到亲本种群之一，以创建两个大型的全同胞研究家族，它们将分离出各自独特的等位基因。这些回交家系将使我们能够使用一种统计上强大的方法来识别其ELP与形态特定值密切相关的基因，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是否有遗传基础，并寻找在两个亲本种群之间序列不同的称为SNPs(单核苷酸多态)的位置。然后，我们将使用我们最有前途的SNP标记来对濒危野生大西洋鲑鱼的尾巴片段进行基因分型，这些尾巴片段保存在共同的孵化环境中。这将使我们能够记录这些濒危三文鱼种群在功能特征上的遗传差异，并可能帮助保护它们。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授权使用的圣约翰水产养殖菌株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.