Further evidence from common garden rearing experiments of heritable traits separating lean and siscowet lake charr (Salvelinus namaycush) ecotypes

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 regulates traits. Here we assess lipid
content, growth, weight, and length variation in full and hybrid F1
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 role 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 pre-determined at birth and
that ecotypes differ fundamentally in lipid metabolism and growth.