Evolutionary Genetics of Early Life History Variation in Salmon: Non-additive Genetic Effects and Local Adaptation

目的：我建议使用分子，人口和定量遗传学方法结合圈养繁殖实验和实地测量划分的相对贡献的遗传，表观遗传，GXE的相互作用和环境的影响，太平洋鲑鱼的早期生活史性状变异。这项工作将最终寻求确定适应性差异的进化遗传基础与早期生活史性状分化的个人和群体。 拟议研究：鲑鱼是我提出的研究计划的显着模式生物：它们在早期生活史特征中表现出极端的变化，这些特征影响了生命后期的关键生殖和迁移行为。一般来说，生命的早期阶段（受精到生命的第一年）经历了非常高的选择压力。早期生存、生长、迁移行为和免疫功能的差异通常构成种群分化，并被引用作为当地适应的证据。虽然过去的研究已经量化了这种变异的加性遗传基础，但探索非加性效应对适应性差异的潜在贡献的研究才刚刚出现。我提议的研究计划将利用我在鲑鱼遗传学、进化生态学和生理学方面的专业知识来描述鲑鱼种群早期生活史特征变异。 一个关键的先决条件是评估的遗传隔离的种群进化分析。因此，我将使用新的NextGen测序方法对微卫星和单核苷酸多态性（SNP）基因分型来测量早期生活史不同的人群之间的连通性。还将使用功能基因多态性评估连接性，因为这些标记可能导致鲑鱼遗传分化的不同模式。 评估“非传统”遗传机制（显性、上位性、表观遗传学、转录修饰等）的作用。在鲑鱼的快速局部适应和表型可塑性方面，我将与政府和水产养殖业的养殖设施合作，使用育种实验、多种饲养环境以及分子和定量遗传学方法。GLIER的CFI资助的EGF实验室为定制微阵列，qRT-PCR（标准和纳米流体）和NextGen RNAseq和miRNA测序提供集中的基础设施。将基因组和转录组学分析与早期生活史性状变异的实地测量相结合，将为我提出的研究计划提供卓越的分析能力和独特的HQP培训机会。 拟议的研究将解决一个核心问题，我们的生活史变化和本地适应鲑鱼的进化的理解：生活史变化反映了传统的适应当地条件，或鲑鱼进化的新形式的生活史可塑性？无论哪种方式，鲑鱼是非常有能力的殖民者，并表现出实质性的地方性状差异。重要的是，我们要描述这种变异，不仅要了解和保护鲑鱼的多样性，还要了解所有脊椎动物的多样性。

OBJECTIVES: I propose to use molecular, population, and quantitative genetic methods combined with captive breeding experiments and field-based measurements to partition the relative contribution of genetic, epigenetic, GxE interactions and environmental effects to early life history trait variation in Pacific salmon. This work will ultimately seek to identify the evolutionary genetic basis of adaptive differences associated with early life history trait divergence among individuals and populations. PROPOSED RESEARCH: Salmon are remarkable model organisms for my proposed research program: they exhibit extreme variation in early life history traits that affect critical reproductive and migratory behaviours later in life. In general, the early life stages (fertilization through first year of life) experience very high selection pressures. Differences in early survival, growth, migratory behavior and immune function often constitute population differentiation, and are cited as evidence for local adaptation. While past studies have quantified the additive genetic basis of that variation, research exploring the potential contribution of non-additive effects to adaptive differences is just emerging. My proposed research program will capitalize on my expertise in salmon genetics, evolutionary ecology and physiology to characterize early life history trait variation among salmon populations. A key prerequisite for among-population evolutionary analyses is the assessment of genetic isolation. I will thus measure connectivity among populations that differ in early life history using novel NextGen sequencing approaches to microsatellite and single nucleotide polymorphism (SNP) genotyping. Connectivity will be also assessed using functional gene polymorphisms, as such markers may result in different patterns of genetic divergence in salmon. To assess the role of “non-traditional” genetic mechanisms (dominance, epistasis, epigenetics, transcriptional modification, etc.) in rapid local adaptation and phenotypic plasticity in salmon, I will use breeding experiments, multiple rearing environments and molecular and quantitative genetic methods in collaboration with government and aquaculture industry rearing facilities. The CFI-funded EGF lab at GLIER provides centralized infrastructure for custom microarrays, qRT-PCR (standard and nanofluidic) and NextGen RNAseq and miRNA sequencing. Integrating genomic and transcriptomic analyses with field measures of early life history trait variation will provide exceptional analytical power and unique HQP training opportunities in my proposed research program. The proposed research will address a question central to our understanding of the evolution of life history variation and local adaptation in salmon: does life history variation reflect traditional adaptation to local conditions, or have salmon evolved novel forms of life history plasticity? Either way, salmon are remarkably capable colonizers, and exhibit substantial local trait divergence. It is important that we characterize that variation to understand and conserve diversity not only in salmon, but in all vertebrates.