Feed efficiency (FE) is a critical phenotype for aquaculture sustainability, yet it is poorly understood at the molecular level. In this study, the molecular basis of FE was investigated using a multi-omics approach to integrate proteome-level data and metabolites associated with differences in feed efficiency. To achieve this, Chinook salmon (Oncorhynchus tshawytscha) were reared in seawater and the liver, blood plasma, and white muscle of feed efficient (EFF) and inefficient (INEFF) fish were analysed using proteomics and metabolomics. By comparing 21 EFF and 19 INEFF fish, 2748 liver and 703 white muscle proteins, as well as 140, 127, and 70 metabolites in the liver, plasma, and muscle, respectively, were measured. According to Gene Set Enrichment Analysis (GSEA) approach, protein synthesis was enriched in both liver and white muscle tissues of the EFF group. Furthermore, in the liver and white muscle of INEFF fish, pathways associated with protein degradation (amino acid catabolism and proteolysis) and glucose metabolism were the most affected processes. The metabolite data showed that pyruvate metabolism in the liver of the EFF group and phenylalanine, tyrosine and tryptophan metabolism in the plasma of the EFF group were enriched. Glutathione metabolism and valine, leucine and isoleucine metabolism were the top enriched pathways in both the plasma and muscle samples of the INEFF group. Integrated analysis of the datasets revealed a connection of metabolites related to lipids and amino acids with catabolism of proteins in the INEFF group. Utilising an integrated multi-omics approach, this study gained insights into the FE phenotype of Chinook salmon and it is hypothesised that protein turnover is a key component of FE in Chinook salmon reared in seawater.

饲料效率 (FE) 是水产养殖可持续性的关键表型，但在分子水平上却知之甚少。在这项研究中，使用多组学方法研究了 FE 的分子基础，以整合与饲料效率差异相关的蛋白质组水平数据和代谢物。为了实现这一目标，奇努克鲑鱼 ( Oncorhynchus tshawytscha) 在海水中饲养，并使用蛋白质组学和代谢组学分析饲料高效 (EFF) 和低效 (INEFF) 鱼的肝脏、血浆和白肌。通过比较 21 条 EFF 和 19 条 INEFF 鱼，分别测量了 2748 种肝脏和 703 种白色肌肉蛋白，以及肝脏、血浆和肌肉中的 140、127 和 70 种代谢物。根据基因集富集分析 (GSEA) 方法，蛋白质合成在 EFF 组的肝脏和白色肌肉组织中均富集。此外，在 INEFF 鱼的肝脏和白肌中，与蛋白质降解（氨基酸分解代谢和蛋白水解）和葡萄糖代谢相关的途径是受影响最大的过程。代谢物数据显示，EFF组和苯丙氨酸在肝脏中的丙酮酸代谢，EFF组血浆中酪氨酸和色氨酸代谢得到富集。谷胱甘肽代谢和缬氨酸、亮氨酸和异亮氨酸代谢是 INEFF 组血浆和肌肉样本中最丰富的途径。数据集的综合分析揭示了与脂质和氨基酸相关的代谢物与 INEFF 组中蛋白质分解代谢的联系。利用综合的多组学方法，本研究深入了解了奇努克鲑鱼的 FE 表型，并假设蛋白质周转是在海水中饲养的奇努克鲑鱼 FE 的关键组成部分。数据集的综合分析揭示了与脂质和氨基酸相关的代谢物与 INEFF 组中蛋白质分解代谢的联系。利用综合的多组学方法，本研究深入了解了奇努克鲑鱼的 FE 表型，并假设蛋白质周转是在海水中饲养的奇努克鲑鱼 FE 的关键组成部分。数据集的综合分析揭示了与脂质和氨基酸相关的代谢物与 INEFF 组中蛋白质分解代谢的联系。利用综合的多组学方法，本研究深入了解了奇努克鲑鱼的 FE 表型，并假设蛋白质周转是在海水中饲养的奇努克鲑鱼 FE 的关键组成部分。