Department of Forestry and Natural Resources, Purdue University, West Lafayette, Indiana, USA.
School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, USA.
Mol Ecol. 2022 Jun;31(12):3432-3450. doi: 10.1111/mec.16492. Epub 2022 May 19.
Genetic evidence of selection for complex and polygenically regulated phenotypes can easily become masked by neutral population genetic structure and phenotypic plasticity. Without direct evidence of genotype-phenotype associations it can be difficult to conclude to what degree a phenotype is heritable or a product of environment. Common garden laboratory studies control for environmental stochasticity and help to determine the mechanism that regulate traits. Here we assess lipid content, growth, weight, and length variation in full and hybrid F crosses of deep and shallow water sympatric lake charr ecotypes reared for nine years in a common garden experiment. Redundancy analysis (RDA) and quantitative-trait-loci (QTL) genomic scans are used to identify associations between genotypes at 19,714 single nucleotide polymorphisms (SNPs) aligned to the lake charr genome and individual phenotypes to determine the role that genetic inheritance plays in ecotype phenotypic diversity. Lipid content, growth, length, and weight differed significantly among lake charr crosses throughout the experiment suggesting that pedigree plays a large roll in lake charr development. Polygenic scores of 15 SNPs putatively associated with lipid content and/or condition factor indicated that ecotype distinguishing traits are polygenically regulated and additive. A QTL identified on chromosome 38 contained >200 genes, some of which were associated with lipid metabolism and growth, demonstrating the complex nature of ecotype diversity. The results of our common garden study further indicate that lake charr ecotypes observed in nature are predetermined at birth and that ecotypes differ fundamentally in lipid metabolism and growth.
遗传选择对复杂和多基因调控表型的证据很容易被中性种群遗传结构和表型可塑性所掩盖。如果没有基因型-表型关联的直接证据，就很难确定一个表型在多大程度上是可遗传的，或者是环境的产物。普通花园实验室研究控制了环境随机性，并有助于确定调节性状的机制。在这里，我们评估了在普通花园实验中饲养了九年的深水和浅水共生湖鳟鱼生态型的完全和杂交 F 代的脂质含量、生长、体重和长度变化。冗余分析（RDA）和数量性状基因座（QTL）基因组扫描用于识别与 19714 个单核苷酸多态性（SNP）的基因型与个体表型之间的关联，以确定遗传遗传在生态型表型多样性中所起的作用。在整个实验过程中，湖鳟鱼杂交种的脂质含量、生长、长度和体重差异显著，表明系谱在湖鳟鱼发育中起着重要作用。15 个假定与脂质含量和/或条件因子相关的 SNP 的多基因评分表明，区分生态型的特征是多基因调控和加性的。在第 38 号染色体上鉴定出的一个 QTL 包含了 >200 个基因，其中一些基因与脂质代谢和生长有关，这表明生态型多样性的复杂性质。我们的普通花园研究的结果进一步表明，在自然界中观察到的湖鳟鱼生态型是在出生时就预先确定的，并且生态型在脂质代谢和生长方面存在根本差异。
