University of Idaho Aquaculture Research Institute and the USDA Agriculture Research Service (ARS/UI strain) have developed rainbow trout families that exhibit high growth rates when fed all plant protein. Our selected rainbow trout strain is a unique model to identify genetic and physiological parameters associated with sustainable plant protein utilization in fish. However, we need to identify the best lines among the selected families of rainbow trout, which can utilize to plant protein (soy-based ingredients) more efficiently. The overall goal of our study was to develop an indirect benchmark to select the families of rainbow trout to enhance the feed efficiency of soybean-based diets and also investigate the underlying mechanism using hepatic proteomics to divulge the proteins involved in the compensatory feeding regime. We tested if feed intake and body weight variations are correlated using compensatory feeding regimes with rainbow trout for genetic improvement of soybean meal based diets (SBMD) utilization efficiency using indirect selection, and to develop alternative criteria to improve feed intake of SBMD in fish. Twelve families (1600 fish, av. int. wt. 30 g) of selected lines of rainbow trout were used in the experiment. Selected lines of trout fed plant protein (50% soy) diet (protein: 41% and lipid: 21%). Firstly, fish were tagged individually and reared in a common environment, fish were on 1st feeding challenge for 4 months (one month each challenge either feed deprivation, FD or refeeding, RF), and growth performance was recorded. Thereafter, fish were separated into four groups (1331 fish) based on individual performance during FD and RF challenge studies. Feed efficiency was recoded for 3 months in all four groups followed by measuring the stability of response to the FD and RF periods (2nd feeding challenge for 4 months) which was the same as the 1st feeding challenge. During the 2nd feeding challenge, liver samples were collected from each group at each sampling point, total five sampling points (initial, 1st FD, 1st RF, 2nd FD and 2nd RF).
Proteins from liver samples were measured by reverse phase liquid chromatography using an Agilent 1260 Infinity Binary liquid chromatography. Spectral files for each sample were analyzed using Spectrum Mill Software (Version B.04.01.141). Peptides were searched against the Uniprot Reference Proteome ID#UP000193380 for Rainbow Trout (Species ID: ONCMY; 46, 447 proteins; downloaded May 2021). In terms of bioinformatic analysis, peptides were sequenced and identified by Spectrum Mill at the MS/MS level, quantification at the MS1 level was performed using the DDA workflow in Skyline 20.2 (MacCoss Lab Software) with a score of 0.9, retention time window of 5 mins, and 5 missed cleavages with transition settings for TOF. Data were sorted and manually consolidated using Excel. Metaboanalyst 5.0 was used to replace missing values with 1/5 of the limit of detection (LOD), normalized using median, pareto scaling, and log transform, and then to conduct principle component analyses (PCA), ANOVA (Fisher's LSD post-hoc test with Benjamini-Hochberg FDR), and partial least squares discriminant analyses (PLSDA). Feed conversion ratio were significant different among four groups. Results revealed that hepatic proteins were significantly affected by sampling point and by groups. Data will be presented. Conclusively, cost of fish production decreased by enhancing the utilization of soybean meal via improving the feed efficiency in rainbow trout.