Through 8 generations of selection, our group has developed a strain of rainbow trout that exhibits high growth rates on an economically and environmentally sustainable all plant protein, high-soy diet. The selected strain is resistant to development of soy-induced enteritis, an inflammatory intestinal pathology that occurs often in high-value carnivorous aquaculture species. To better characterize the physiological mechanism behind the superior performance of the selected strain we compared the homeostatic intestinal gene expression of the select strain to that of a commercial control line of trout. Samples were collected at early life stages known to be critical in the development of host-microbe interactions in the gut of rainbow trout. All female cohorts of both strains were reared alongside starting from eggs. Intestinal samples from 5 fish per group (2 fish strains 2 developmental stages 20 samples total) were used to generate mRNA selected stranded RNA-seq libraries for high throughput sequencing. Reads were quantified at the transcript level prior to evaluating differential transcript usage and differential gene expression between the two strains of trout and the developmental stages. Overall design: An all-female cohort of the select and commercial strains of rainbow trout were reared in flow-through spring water (15°C) starting from eggs. From first feeding to the conclusion of the experiment, both strains received a commercial trout starter diet. Intestinal samples were collected from both groups after ten days of feeding which occurred at 20 days post hatch (dph), and at 65 dph, which is just prior to the time when we traditionally switch the fish to an all plant protein diet. RNAseq libraries were prepared for five intestinal samples per experimental group for a total of 20 samples.