Hundreds of Genes Remain Differentially Expressed after a Single Generation of Domestication

The genetic underpinnings associated with the earliest stages of plant and animal domestication have remained elusive. Because a genome-wide response to selection can take many generations, the earliest detectable changes associated with domestication may first manifest as heritable changes to global patterns of gene expression. To test this hypothesis, we measured differential gene expression in the offspring of wild and first-generation hatchery steelhead trout (Oncorhynchus mykiss) reared in a common environment. Remarkably, we found that there were up to 723 genes differentially expressed between the two groups of offspring. Reciprocal crosses revealed that the differentially expressed genes could not be explained by maternal effects or by individual differences in background rates of expression. Gene enrichment analyses revealed that adaptation to the novel hatchery environment involved responses in wound healing, immunity, and metabolism. These results demonstrate that the earliest stages of domestication involve massive, heritable changes in gene expression.